Hi there. I own and use both the Icom 765 and the FT-990. I've owned them for over 15 years, and I can add the following as a "user", not as a "fan" or "basher".. hi hi..
The 765 has all the mod's and fixes and filters, except the roofing filter and sidetone mod. I use it primarily for 160 mtr CW DX'ing. It has the better front end under contest conditions. Overall, it does have a better receiver than the FT-990, but there are other things to consider as well. I've had to fix a few things in the 765 along the way, nothing major, but servicing was required. AM reception is excellent! QSK quite good and the cascaded 500 Hz or 250 Hz filtering is bullet proof. The internal antenna tuner does not seem to be as forgiving as the FT-990's, but that's what external tuners are for!
The FT-990 has been 100% reliable, never any fixing or "tweaking" required. It has all the filters in it. The internal antenna tuners works well beyond the 3:1 spec, but doesn't tune "everything". I use it for RTTY contesting and also for PSK. I like being able to use any filter in any mode. With a RigBlaster Plus, AFSK RTTY is a breeze, with no distortion (i.e. no ALC deflection!). The SCAF filter takes the hiss out and is useful despite being out of the AGC loop.
Overall, the FT-990 is a bit "easier" to use but the receiver in the 765 is a bit better, at least for what I do. For me they are both keepers and are in use daily, depending on what band, mode, or contest I want to play around in. Just my two cent's worth, your mileage may vary! 73 - John (WA1GOS)