Personally I think an automatic transmission is a complete waste in these cars, or any performance car for that matter. People always say "an auto is more consistent", or "an auto is faster in the 1/4mi", and I call BS on both of these statements every time. People compare a professionally built automatic transmission, that was built to go in a drag car, and has a higher stall converter, and upgraded frictions, and a modified valve body and where the shift points are tuned in, with a stock 5-speed car and say "see, its faster and more consistent". Take that same car and put a close ratio Jerico 4-speed in it, and someone who knows how to properly drive a manual trans car, and see which one makes it down the 1/4mi faster or is more consistent now? I've never had a problem being more consistent in a manual trans car than in an automatic, and my opinion is that if you don't know how to drive a manual trans car, then you don't know how to drive at all, and if you don't know how to drive a manual trans car consistently, then you don't know how to drive consistently. Don't blame the transmission if the car is not consistent, blame the driver.
As far as these cars go in particular, if you were unhappy with the 4R70W in the 94, then you will be sorely disappointed with an AOD (aka a DOA trans). With stock power levels and in stock form, a DOA trans can last a long time, but they don't take kindly to having more power put through them, and they don't take kindly to WOT shifts, and they don't take kindly to the TV cable being slightly out of adjustment, and they don't take kindly to steeper rear end gears, and they don't take kindly to higher stall converters that still have a lockup, and they don't take kindly to higher trans temps that come with a non-lockup converter, and... well you get the idea. So before you are going to put any more power through an AOD, you need to either convert it to a 4R70, or drop $3K on a built trans. The 5-speeds are not without problems, but I'll take an M5R2 over any automatic any day. The M5R2s were originally designed as a truck transmission, so the gears themselves are very strong, and I have only heard of a few people actually doing any damage to them, however the synchros really aren't up to the task of speed shifting at 6K rpms. On the street under normal driving, they will wear out quicker than in a T5, but even on a freshly rebuilt trans, you might find that the gears grind when taching out 1st gear and grabbing 2nd. Also, the stock shifter is garbage, and in my opinion is the sole cause of the "notchy" shifts that everyone complains about with these transmissions. With a B&M ripper shifter, my M5R2s are just as easy to shift as my buddy's T5 or my Tremec 3650, both of which also have aftermarket shifters. That does bring us to the other problem with the M5R2 which is parts availability, or rather unavailability. The B&M shifter was the only performance shifter ever made for this trans, and it has been discontinued, so if you get a 5-speed car you will need to track down a used one, and since they are a necessary mod for any 5 speed car, and are not going to be produced anymore, used ones typically go for more than they did when they were new. Also, if your trans does require a rebuild, synchros are also unavailable, and the only option is to use ones for an F150, which will work but don't have the fiber lining, so the synchros that were not really up to the task before will now be even worse. Also, the gear ratios in the early style M5R2 are not ideal. 1st and 2nd are very steep, which is a lot of fun on the street, but then there is a very disappointing huge jump going to 3rd, then 4th is 1:1, and 5th is .75:1. The 94/95 M5R2s had a shallower 1st and 2nd gear, with 3rd, 4th, and 5th being the same, so all the gears are more evenly spaced, but that also means that with the stock 2.73 rear end gears, you are not getting as much torque multiplication out of the hole as the earlier style trans. Compensating by changing the rear end ratio will work, but then you still have only a .75 5th gear compared to say a T5's .67 or .62, which is better because how often are you taching out 4th gear and looking to grab another gear and keep accelerating? Ultimately, the best option would be a T56 swap, but for a street car I think you'll be quite happy with a good condition M5R2 with a B&M ripper shifter.