Don't take this the wrong way Malenko.... but the fact that you didn't like the prior 3d games (which weren't fantastic but still pretty good) shows that you have rather poor taste in MK fighters anyway.
I think the problem is you compare the MK games to previous MK games. I do that too, but I also compare it to whatever else is out at the time. The 3d games were DEFINATELY better than their competition. We have suffered through a long drought of fighting games... just be glad they are good again. 
Dont misunderstand me, MK4 was definately not the high-point of the MK franchise, but it wasn't a low point either. Worse than MKII, UMK3 and the other 3d interations, but better than Armageddon and possibly a few others. It was a transition game and therefore had a lot of problems, but I can't really see bashing it when it added so much to the story and gameplay mechanics of future games.
MK9 spoilers below:
I didnt really like the MK4 story either, Quan Chi and Shinnok just dont appeal to me. You can tell that the MK guys didnt really like the story of the console MKs because they pretty much ignored that arc (other then Quan Chi and Shinnok) in the new MK game and focused more on the MK1 to Umk3 arcs. I'm sure when MKX is released around next year they'll reference some of the "other stuff" but it appears they are abandoning a lot of that canon.
As for the console MKs , as fighting games they were ok, but as Mortal Kombats I hated them. I liked the first one of the 3 the best, but I cant say I was a fan of how it played, how it looked, or who was in it. Armageddon while bad was just fan service, so I didnt have high hopes. Special Forces was the low point, with MK4 a close second, and MK:Sub Zero a distant 3rd.
My real issue with the previous console MKs, was they felt like a different game staring MK characters and the gameplay was SOOO SLLLOOWWWWWW. What mechanics of MK4 made it into other games? Picking up random objects to throw? Nope. Pulling out weapons? They canned that too. low-poly & low textures? thankfully gone. MK4 was also the last MK game to use the "standard" MK button layout.
Compare MK to whats out at the time? sure. MK4 came out in 1997. That puts it up against Tekken 3, Soul Edge Ver II, Street Fighter Alpha 3, Street Fighter 3, Street Fighter EX Plus, Rival Schools, Last Blade, Final Fantasy VII (it came out in 1997 but I was just seeing if you were paying attention), Virtua Fighter 3, and Vampire Savior 2. MK4 is probably at the bottom of that list.
As for them abandoning 3D in street Fighter "quickly" it was about 5 years between the release of Street Fighter EX and console release of Street Fighter EX 3. The naming convention was funny on the EX titles though.
Street Fighter EX -original release
Street Fighter EX plus -"super update"
Street Fighter EX plus a - console release of SFEX+
Street Fighter EX 2 - arcade sequel
Street Fighter EX 2 plus - "super update" & console release
Street Fighter EX 3 - console release
Street Fighter has always had the best names. Street Fighter Zero 2 dash gold, Super Street Fighter II Turbo X: Grand Master's challenge, Street Fighter II Dash Turbo