Wow, the Mopar AEM doesn't even have a base tune? I figured for the price they ask for that they'd at least put in the stock Dodge tune. I think pretty much any aftermarket system will be equally hard to set up in the software. The Megasquirt just doesn't have any option for a plug and play style harness, you'll have to make your own. Not sure if the FAST setup comes with factory connectors or not.
I didn't have much trouble doing actual fuel tuning with my Megasquirt, you just look at O2 feedback (if you have a wideband) and adjust the fuel map values, though you have to have all other stuff right first. My TPS sensor was really noisy, so I was trying to tune my setup with constant "accelerator pump" enrichments kicking in without me knowing. Once I sorted that out it started reacting more like I assumed (ie when you change values it actually makes a difference, lol). You can pay for auto tuning capabilities for the Megasquirt as well, though they don't recommend using it for a base tune, more for fine tuning a stable setup.
The cool thing about the Megasquirt setup is really what all you get control of, assuming you want that. On the Megasquirt I have (MS2 Extra) I can pick what kind of O2 feedback correction I want (simple correction or algorithm based), what kind of idle control I want (maintain rpm with IAC, just use IAC for warmup, or nothing), batch or sequential injection (add on pieces needed), TPS or MAP based accelerator enrichment, etc. The other neat thing is that the software is constantly being updated, so new features get added every once in a while. I don't mean to sound like a salesman for them, I just thought it was fun to be able to do that much myself and I like learning how to do things myself so I'm not waiting on other people. I started my setup simple and keep adding features one at a time when I get all the other things working.
I've worked with an AEM for a college project and it's similarly powerful. You get a lot of control and you can run all sorts of things with the AEM box, though I don't know that it has as many options as a fully equipped Megasquirt. The tradeoff is generally that most of the options that the AEM doesn't let you control are ones that could potentially damage your engine if you get them wrong or that you wouldn't bother 99% of the time anyway.
You can get into a Megasquirt fairly cheap compared to other aftermarket systems, but by the time you include all the add on pieces you might want and all the wiring and other parts that you need you don't come out too much cheaper than something like the FAST EZ EFI system (though you can't tune that one). If I didn't get mine for a steal I'd still probably be running around with a carb.
