It's not feasible to manage a website catalog, eBay catalog, and Amazon catalog these days. M2E Pro is the solution to manage all of these channels on pretty much an automated basis. That in itself is amazing. It is feature rich, you can customize whatever you want, and it works...most of the time.
That said, this software is resource heavy and can be complex. I've been using it for 2 years and while I have a good handle on it, I occasionally run into issues.
For example, every time we have to update the software (which is fairly frequent), it crashes our site. It never installs correctly for us through Magento connect, and when installing manually, it usually crashes something. We have to disable the entire extension while we wait for support to fix the issue (I'll get to that later) so eBay and Amazon channels have to be turned off and we lose sales.
Another example is that we'll notice things stop syncing all of a sudden. Usually, it is a corrupted database table that we have to repair, but support has refused to help us with this issue. They claim that "their software does not contain anything that would crash database tables." Except...it's M2E pro's tables that are crashing, and 2 - we have this software installed on several Magento installations (all different) and it happens on every single one.
My main gripe is support. There are some amazing extension developers out there who offer fantastic support - always prompt, extremely friendly, and willing to make an effort.
M2E Pro's support does the minimum possible. Yes, support is there, but be prepared to get frustrated with them and fight them to fix it. They'll tell you issues are related to other extensions and that there is nothing wrong with their software. They'll refer to you to their wiki which contains basic instructions you already knew and passively insult you like you don't know what you are doing. You're pretty much stuck in this case.
Here's the thing - Magento is complex and the average installation has many extensions installed. Every other developer I have worked with has done their best to figure out conflicts...they genuinely show an effort - not only for our benefit, but to build their own library of potential conflicts. There's that and the fact that I know that some issues are M2E Pro itself and not conflicts....blaming other extensions is just the easy way out.
Do I still use the software? Yes. But I'm not counting on it anymore and I make sure our website generates the majority of our revenue so that we're not dependent on eBay & Amazon.
The truth is that this extension has some of the most potential of any extension out there. If someone else was running the support, it could be so much better.