I know this thread hasn't been active in a bit, but I have both of these projectors at the moment and wanted to give some comparison.
The 3500 definitely has better blacks and contrast, especially at night with minimal light, it's obvious.The 2040's blacks look dark grey, the 3500 seems to be real black - not void black, but black
The 3500 is about as bright in medium as the 2040 is in high. The 2040 only has eco and normal, while the 3500 has eco, medium, and high. Both projectors are pretty noisy on high/normal. Medium is slightly noisy, but really not audible even with soft volume coming though your speakers. The 3500's high adds extra pop (10% more in high) on top when it's really needed.
The 3500 doesn't have frame interpolation. However I don't think the frame interpolation is very good on the 2040: it jumps every bunch of frame, and even on low has a very soap opera look - I think on low it should really just smooth panning scenes but not really alter the movie "feel"
The fine vs fast mode on both projectors does decrease the lag, and the picture gets a bit more sharp and jaggy in fast, but during gameplay, it's very hard to notice. Lag is noticeable (barely) on the 3500 in fine. The 2040 has no lag I can detect in either mode.
The 2040's detail enhancement is niceish. The 3500's super resolution is better - really makes detail stand out - although I wish it had more than 5 options.
3D on both of these projectors is great and bright. Edge to the 3500 because it can get brighter. Both have very minimal crosstalk when there are bright white small images on a black/dark background. To me it seems the 3500 has a bit less - but both are minimal.
The 3500 has panel alignment which is great, and more placement flexibility with larger zoom and true lens shift which is great too.