I been running a GT2560 for about 5 years without any issue. I've disconnected the wastegate so now it breathes more freely with upto about 20psi of boost and lower EGTs post turbo.
First thing I noticed after being fitted was the motor reached peak power much earlier and so quicker gear changes. I'm looking forward to fitting a WTA IC as I think it will make a significant difference (the motor runs smoother on cool mornings).
I've briefly driven Inside's Perentie on the beach, which I think has a GT2260 with a ATA IC. I think it ran a bit better/smoother than mine but quite similar (unknown if this was due to turbo, IC or other factors).
Either would be a very good choice IMHO.
Im selling top mount Isuzu manifolds for either T25 or IHI if you need one. I should put them in the markets section.

