Yo Snipe,
You make some good points. I'm not sure why you're bringing size into the equation -- in general, being large is almost always better than being small, and most PCs are going to be small or medium-sized. (At least, in core campaigns. I personally don't dig on non-standard-race PCs, and if playing a large PC messes up game balance, then all the more reason not to allow large PCs except when they're polymorphed.)
Let's look at what Chainy needs:
1) Exotic Weapon Prof: Spiked Chain
2) Expertise (Int13+)
3) Combat Reflexes (say Dex13+ to make real use out of it)
4) Improved Trip
Now, I don't see a ton of people NOT having a Dex of 13+ if they're playing a combat character. The Int13+, though, costs a bit. If you're going with Point Buy, that means fewer points left to get the Strength higher and up that Dex into nastyland.
You're giving up damage and/or defense (using a greatsword or using a bastard sword and shield) for a cute trick -- the reach and trip deal. And you're buying feats that make that combo worthwhile -- which, in my book, is fine. Heck, I could trip you with a heavy flail, then quick draw a greatsword next round and go all Power Attacky, and that would be pretty nasty, but we don't hear complaints about it.
The other factor here is the sheer mathematics of it. I'm definitely out of my league, here, but from unscientific anecdotal evidence, I always found that having to make two rolls really lowered my chances of success -- and with the trip dude, you have to make THREE rolls to get this right:
1) The touch attack to hit
2) The opposed Str/Str or Dex check
3) The attack roll on prone-boy
Touch attacks aren't guaranteed hits, not with Blur and Displacement and all that fun stuff. It's still a LIKELY hit in most cases, but our average guy probably needs more than a 1 to touch-hit the single, equal-CR opponent he's using this against.
The opposed check allows the opponent to use whichever score is better. Now, our attacker gets a +4, so he's got a slightly better chance -- but if it's two fighters of equal level, and one fighter has the chain while the other fighter has a greatsword, and they're both Point Buy... who do you think has the higher Strength? The attacker has a DECENT chance of tripping the person, assuming his first roll works.
Finally, the prone attack, upon which he gets a +4 to hit. Again, probably a good chance of hitting.
So, for all that, we've got LIKELY times DECENT times PROBABLY... which adds up to MAYBE, in my book. And since I'm at work, that's as scientific as I'm getting. I'd love to see somebody do the math on it.
Our attacker is doing that instead of making one simple attack roll that, most likely, could have hit for damage right there and saved time. Yeah, his target's prone, now, and that's good -- and when the guy tries to get up, we can try to make another three rolls. But in my experience (purely anecdotal), you're gonna botch one of those rolls somewhere eventually.
I'm not saying it's a bad strategy against one single opponent, but I can't say that I'm losing sleep over it, either. When I DM'd a 3.0 dwarven fighter with improved trip, he used it to great effect on every squib we encountered, but he always settled in for power attacking when he faced something challenging.