I feel like it would be an exceedingly bad idea if I responded to this, but … fine.
As a disclaimer, I’d imagine that there are a number of ways one could transform into a pokémon, and each one may carry its own unique … consequences. For example, if you transformed via extreme psychic exertion, immediate resurrection, or just plain magic like some folklore and urban myths about the origins of certain pokémon imply, that would be entirely different than, say, accidentally merging yourself with your test clefairy via a teleportation experiment gone horribly awry. Which, as we all know, I would know nothing about.
Regardless, I’ll do my best to keep my speculation as general as possible.
For the most part, the one thing humans have over pokémon is will. It’s why pokémon turn to us for training; we’re simply inordinately tenacious. For this reason, I’d imagine—because I certainly don’t have experience in this matter whatsoever—that if a human were to become a pokémon, then yes, they would retain their intelligence. Even in situations where (hypothetically speaking) it would actually be more like the human and the pokémon were sharing a body, it’s very likely that the human would largely be in control during those situations, due to their generally stronger will. I’d imagine that you would still hear your pokémon’s thoughts, but they would simply be more or less another voice in your head that would be somewhat distracting in your efforts to undo such an unfortunate situation, but it wouldn’t necessarily be unmanageable.
You could, of course, also gain a pokémon’s instincts at first because the entire situation would be rather jarring and confusing until you grow used to your body, so if you, say, merged with a clefairy, you may find yourself oddly skittish, repulsed by loud noises, and brimming with energy under full moons until you learn to ignore certain unpleasant sensations. On the positive side, grasping your pokémon-based powers and techniques may come easier than one would think, as those tend to rely on instinct and intuition more than anything else. (On that note, I would imagine that Metronome would be a terrible thing to experiment with, but I would know nothing about this.)
Now, when it comes to being caught, in theory, because you share a genetic code with actual pokémon, yes, a poké ball may just work on you, which is why it is likely of the utmost importance that you establish that you are not, in fact, a pokémon, usually by simply speaking to any approaching trainer (such as the young trainers who have, in this hypothetical situation, managed to break into your lab at a highly convenient time).
As for other pokémon, it really depends. Your own will likely recognize you by scent (that and you would presumably tell them of your situation). Wild pokémon may not be so discerning. Some may be confused if they can smell the human in you, but others—especially bird pokémon such as fearow—may only see you as a pokémon (which would be rather unfortunate if you happened to mess up an entirely unrelated experiment and merged yourself with its primary food source, rattata … which, again, I would know nothing about).
On the positive side, generally speaking, a number of your senses may be sharper, and you will temporarily gain a unique perspective (pun most definitely intended). On the negative side, the actual transformation process may sting a bit, the act of getting used to your body will likely be awkward, and the journey towards restoring yourself may be tedious and require bribing young trainers.
Again. Not that I would know anything about this.
The Pokédex According to Bill 