I have an LT and I still pick the TRX250R. Best ever made all around quad IMO.
They have a huge aftermarket. They have great frame/suspension geomotry.
Dirtwheels just did a shout out with a 86 250r and a 2009 450r and they came out in a tie. So a 20 year old machine that can still hang with new sport quads.
The LTs are great machines also. But it is harder to find parts. The motors arent as strong and not a big aftermarket following. The 85-86 LTs are almost impossable to find aftermarket stuff. The 87-90 are easy to find parts for but still has the suspension with a bunch of linkage. The 91-92 have a MX style rear suspension.
One thing you have to think about is that back in the early days of the quads, the factory Suzuki team used Laeger frames with TRX250R geometry. So Honda had sopmething right.....