If I were any good at drawing, this would be illustrated. But I'm not, so it isn't.
First of all, if Pokémon were made real, battling them would pretty much be out of the question, since it would likely be considered animal cruelty (akin to cock fighting, etc). Plus, you'd have lots of Daily Mail readers bitching about how genetic engineering is unnatural or whatever. But for convenience, I'm ignoring these facts.
Second, I should point out that I'm not a biologist, so if I get anything wrong - Mrs Elston, Mr Bestford, I apologise.
All this will assume current or plausible future technology. This is not to say that some of the things I may dismiss will always be impossible. You never know really.
So there are three key things you need to work out if you're making pokémon:
1) aesthetic correctness
2) "evolution"
3) "moves" - whether they're possible and how.
Possibility
First and for most you have to ask, is a particular pokémon possible at all?
And for this I mean like, for example, ghost pokémon - no, ghosts don't exist. Pokémon made of solid stone or steel - no, I can't really see how that would work.
But aside from those, there are some that would be possible if you made minor (or slightly major) changes.
One example - pokémon that are perpetually on fire. Aside from health and safety issues, I can't see how you'd make it work. Especially for Ponyta and Rapidash - a horse with a flaming mane? I can't see it ending well. Unfortunately, if you take away the fire, they're pretty much just horses.
Similarly, things like Blastoise - the giant turtle with the retractable metal water cannons in it's shell - definitely needs some tweaking. Maybe if they were fixed, bone-based cannons that were some how attached to something akin to a blowhole?
With regards steel/stone pokémon, it could work as either (pseudo) sentient robots for the likes of Voltorb, Magnemite, etc; or in the case of say Onix, maybe a large snake with a hard, rock-like armor. And similar for other rock pokémon.
But these tricky ones aside, there are plenty that are quite plausible.
Creation
There are two methods of creation, as it is. In the cases of (mostly) aesthetic variations of pre-existing animals, you could get away with selective breeding, at least to a greater extent.
This would work best in, for example, some bird pokémon like Pidgey, Swellow, Starly; or some reptiles like Ekans, Arbok, Kecleon..
And in some cases, like Eevee - setting aside the whole evolutions thing (more on that later) - you could quite easily have an Eevee by just buying an appropriate breed of dog (pomeranian?) and grooming so as to give it the correct appearance.
Similarly for things like Teddiursa and Ursaring that need little to no change from pre-existing animals.
In terms of markings, some may be harder to breed for definite recurrence - i.e. there'll be a lot of randomness in specific markings. And there are some colours, or fur in particular, which I'm not entirely sure at possible naturally.
For ones that don't significantly resemble existing animals, but resemble extinct animals such a dinosaurs, it'll be a wait. Beyond that, you may struggle.
Things like Bulbasaur, I don't know how you'd graft a living plant onto a reptile - unless of course it's not actually, physically a part of the reptile, but has a symbiotic relationship with it. Somehow.
Anyway. I could go through all the pokémon, but frankly I'm not going to. 600+ pokémon? Pfft!
Maybe some other time.
Evolution
First of all, the pokémon definition of 'evolution' is quite different to Darwinian evolution. It's wrong for one thing. But that's incidental.
The whole evolution thing is a pretty big part of pokémon. But I'm just going to go ahead and say this - dramatic, instantaneous metamorphosis is ridiculous and impossible.
Realistically, it has to happen over an extended period - so for example, with the Pidgey evolutions the change would work gradually, and you'd have intermediary phases between it and Pidgeotto and Pidgeot. And this would work for a lot of pokémon, albeit with a little creativity.
Insect pokémon, at lot of them mimic real insects pretty well anyway. They just speed things up, missing out the gradual change.
Obviously, this evolution would be time-dependent rather than as a result of 'experience'. Which does take the fun out of it slightly, since it would make the evolution of you pokémon feel like less of an achievement.
Plus it would mean that your little sister could have a Gyarados just by catching a crappy little Magikarp and waiting. And besides that, Magikarp's evolution would be less impressive if it were gradual. Unless some sort of cocoon like deal were used.
The more 'magical' means of evolution - i.e. stones, trading; you might be pushing it.
I suppose, in the case of stones, they could trigger specific genes to activate - either by being radioactive, or some such crap - and again, over time, that would lead to a particular final outcome. Trading, I can't see that ever having an effect. Certain held items, pretty much the same deal as the stones.
Battling and Abilities
Okay, so assuming your pokémon doesn't win a battle, sustaining only minor injuries (if any), in the real world there are really two outcomes to a battle:
1) Unable to continue - either by being knocked-out, comatose, crippled - and I mean genuinely crippled. These things could potentially be healed over time - but not as instantaneously as the Pokémon Centre does - and odds are in most cases they'll never be able to fight again.
2) Dead.
Normal, Fighting, Flying, Rock, Steel, Dragon, Ground, Bug,.. - pretty much any physical attack, fair enough. It may take some training or may have to be taught, but still.
Certain attacks may not be possible for certain animals. Whatever. It's straight-forward enough.
Most defensive attacks are pretty straight-forward as well. Falling asleep in the middle of a battle - unlikely. And I doubt the sleep's restorative power would be worth it.
Special attacks. Now:
Psychic - might be vaguely possible in the future. Maybe. But that might be pushing it. Would likely be in the form of some implantable technology.
Electric - most plausible of the specials, given that creatures such as electric eels already do this sort of thing, albeit short range. You might be able to enhance that.
Water - possible, in so far as it's possible to manipulate any water that may be around you. Out of water, you might have a problem, unless they can store it somehow, or you just carry bottles of water with you.
Ice - similar to above. You can manipulate surrounding ice/snow, but I can't think how it'd work away from snow.
Fire - not that sure. Suggestion have been put forward for how fire-breathing dragons could work. Maybe by storing naturally produced gases (methane, for example) and creating some sort of spark using claws or teeth or something as a sort of flint. Hell, hold a lighter in front of a cow's mouth and wait - fire-breathing cow! So yeah, it's mildly possible.
Grass - again, it's manipulating your environment, or possibly using any foliage that might be a part of your body.
Poison - fairly self-explanatory.
Ghost - no. Non-physical Dark - no. Other specials of the more physical attacks - might be pushing it
And again, all of this comes down to some genetics, and some training (as appropriate).
Abilities, some are plausible - such as having good balance, being flame-resistant, etc - while others are slightly less so - like levitating.
Bonus: Shiny Pokémon
These are Pokémon with alternate colouration - a minor aesthetic difference. So realistically, while we're genetically engineering them, we can give then a recessive gene, or else a set of genes prone to mutate in rare instances - that will cause the change in appearance in approx. 1 in 8192 individuals of a species.
Technology
Pokéball - for the foreseeable future, out of the question. Not until (or unless) we develop transportation and similar derivative technologies. I wouldn't hold your breath.
Obviously, this presents a problem - in the cases of the larger pokémon, where do you keep them? In a good handful of cases, there are Pokémon too large to keep even in your back garden.
So either make them such that they don't exceed some size (say, some zoo friendly size) or else try to avoid those which will cause this problem.
Healing - as discussed above, I can never imagine a way of healing potentially fatal injuries in 5 seconds or less. We're talking standard veterinary care - albeit in the future slightly more advanced. And the vets would, first, have to be trained to treat Pokémon.
Potions - I can't think of a real world equivalent, besides general curative pharmaceuticals.
Paralyse heal - only if it's, say, hysterical-paralysis or down to muscles tightening or something of that sort. You certainly can't spray a magic potion and heal broken bones.
Awakening - maybe. Though it most cases, just waiting would be sufficient.
Antidote - i.e. anti-venom, sure, but I don't know if an all-in-one is possible.
Burn Heal - Yeah, but it won't be instantaneous.
Ice Heal - again, just giving it time would suffice, or else wrapping them up for quicker results. Any worse than that, your Pokémon's fucked, unless it can produce it's own anti-freeze.
Full Heal, Full Restore and berries - don't push your luck.
Conclusion
So some pokémon aren't entirely implausible. Which is nice. Others, no chance.
As Joe pointed out, there are risks with genetically engineering pokémon. Lord knows we wouldn't want a Mewtwo on our hands. (Or would we?). Although, given all the rigor that goes into genetic engineering, we shouldn't have such dramatic problems.
But it's worth keeping in mind, there is always the risk of unforeseen and unintended consequences. Ideally, you'd want to make them - at least initially - on a Jurassic Park -type island, where they'd be contained with minimal risk to the general public.
And as a final thought, if we keep in mind that scientists haven't made unicorns yet - which is a fairly minor alteration to a pre-existing animal - we might be waiting a while.
Oatzy.
Bonus - various photoshops of 'real' Pokémon:
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