No comparison. I used to have a honda recon before i bought my warrior (same engine, frame, suspension as 250ex), and my brother still rides a 250ex. The 350 will burn it off the line, and as they gain speed, it starts pulling on the 250 even faster. The top speed of the 250 is around 45-50 mph because of the gearing (and lack of power to go faster if the gearing were any higher).
Number wise, I think the 250 has 13 hp at the rear wheels, and the 350 is around 20.
Top speed of the 350 has been reported at 62-68 depending on surface, conditions, rider weight, exaggeration of speed, etc (actually i've heard someone claim 88 stock which made me laugh because my 700 with mods and the speed limiter removed won't hit that).
But the suspension will also be better with the raptor, you've got longer travel and shocks that are better suitable for aggressive riding. And you'll have a rear brake that will work!!! YAY!! I can't remember one instance that i've rode a shaft driven honda that had a decent working rear brake.
I'm not in any way putting down the 250ex's though, they are great for what they are designed for, a fun, entry level, easy to maintain machine. The 250ex is actually one of my favorite machines to ride because you can beat the crap out of them all day and they just keep going without hesitation, and they're a blast to throw around in the woods. If you are good with your 250, don't be surprised if it takes a while for you to match your old lap times in the woods with the 350. To be quite honest, i think I can probably still get faster lap times out of my brother's mildly modded 250ex in the woods tracks, than I can get on my raptor 700 because I can push it to the absolute limits without having to worry about overpowering it or losing control (or wrecking my $8,000 quad). Maybe that makes me sound like a crappy rider, but that's just the way things work sometimes.
You should be happy with the trade though, when I got my warrior I was very happy with the performance compared to the 250. As is with anything else though, it's never fast enough for very long though.