I don't do a lot of animation and dynamics so I rarely batch render as I work with stills but I know rendering avi in Maya is a bad idea so stick with iff and tiff. My tech skills were so poor when David first tricked me into learning Maya, for this reason I've struggled more than most people would with technical errors like this and I just wanted to give you some advice here because Maya will throw up a fair few errors and 99 percent of the time I've found that it's me as a user and not the actual program that is to blame. And it's really difficult to say what the problem is when you're new to a 3d app with time you start to recognize patterns and it gets easier to get past these things. So as far as it's possible try not to get too hung up on small issues and if you can't figure it out save your scene and start experimenting with everything that could possibly be throwing up an error. You should never just turn things on all over the place, but it's also important to try and get to know the technical side of the program and the only way to do this is by trial and error. It goes for everything in Maya, instead of changing a slider by 0.1 to figure out what it does crank it up to 100 and you'll get it straight away. Also for rendering errors it's really important to read what it says in your script editor and try to make sense of it, as well in your render view window you have the option to run render diagnostics and this is so helpful so use it, it will tell you what it wrong pretty much every time you get stuck.
For AE or other compositing software I can't really say which ones best as I don't use any but I think it comes down to picking an app and sticking with it, once you have it under control information transfers well between them. For version upgrades someone who used Maya 4.5 well would not have a lot of difficulty getting used to Maya 2011, certain fields change more than others but the application remains the same. The only reason for why you would want to use a specific 3d application as a hobbyist would be because you liked the workflow better in one, and as someone who wanted to work in the industry because certain industries use certain apps more than others. An example here would be archvis which I'm reading a lot about atm where the industry uses mainly max and vray, so if you were going for a job here you'd be better of with max than maya as the studio you would work for would most likely be using max, but someone with maya skills would be able to transfer the same knowledge and have a good grip of max within weeks. As studios use proprietary software anyone who gets a job at a large studio has to learn to use their in house tools as well at which point your software is less relevant. Huge resources go into creating custom apps and hundreds of programmers can be employed to work on this for one specific movie. Next time you see a pixar movie in the end credits look at the list of names for 3d artists and then the list for programmers
So my tip would be to stick with AE if this is what you have, this is also what we'll produce training for as David uses it. We might do nuke and shake as well as this is what our animator works in, the thing with these guys who's worked in the industry for many years is that it's not rare that they have an arsenal of 10-15 apps and it's not because they sat down and decided to learn them all but because they worked at many different studios that used different apps so they were forced to learn the in house software at the time.
Sorry for the novel again