Well, on a personal note, MKDA did get me back into MK after a while away from the series, and it brought me to this site for the first time, so it has a special place in my heart for those reasons anyway...
I won't bother comparing it to the 2d MK's, because that's been done to death on these forums, but I will compare it to MKD, because before I came to this thread my prevailing opinion was that MKD was better
I didn't think they "went away from that engine" as you say, necessarily, but there were some changes between MKDA and MKD that I didn't like, come to think of it. Contrary to what one of you implied, the re-inclusion of the traditional uppercut in MKD turned out to not really bring much to 3d kombat like it did in 2d. I think 3d MK was better without it. Also, I much preferred MKDA's natural combo timing as opposed to MKD's "press them as fast as possible." I know they were trying to get back to the way combos were done in MK3, but at least in MK3 the characters on screen performed the combos almost as fast as you pressed the buttons. The lag time between the button-pushing and the on-screen animation in MKD was off-putting. MKDA was much better in that regard (in most cases, anyway *glares at Cyrax*). I didn't much like the impale moves in MKDA, though (especially Kitana's where you lose her fans even if it doesn't connect), and I'm glad they took those out of MKD.
Character-wise, there seemed to be more classic characters in MKDA than MKD, and I liked that. It was nice to see some MK3 characters return in MKD, but I didn't like that so many MK1-2 characters were missing unlike MKDA. I understand it had to be done with where they were going with the story, but still. Also, I actually liked the death of Liu Kang in MKDA, and not because I'm a Liu Kang hater like some of you. I just thought it was a great twist in the story. As far as new characters go, MKDA's new characters were much better story-wise, but not as good fighting-wise as the MKD new characters. It was nice to see that the few new characters that were actually good (Bo' Rai Cho, Li Mei, Kenshi) actually stuck around for MKD.
I didn't much like the idea of unlocking characters with koins. This is somewhat mitigated by the fact that I could go online and find out exactly which koffins had the characters, but it's still annoying. I much preferred MKD's idea of unlocking characters by performing specific tasks in Konquest.
One thing I didn't much like in MKDA was the fatalities. It's the only MK other than MK1 where each character only had 1 fatality. You would think that with so few fatalities, the quality would at least be good. Instead, we got Quan Chi's infamous neck stretcher. Ick.
Konquest mode was nice, but I much preferred MKD's version. It would be nice to see something like that one in an MK game again.
All in all, it appears from this examination that MKDA was actually better than I've been giving it credit for. I'm going to have to go play it again...