I also own T5, MgT1e, and MgT2e (at least what has been released so far) and went through the same decision process you are about 2 years ago when I started my campaign. I had not played Traveller since the CT days so I took a look at all the versions to determine which I wanted to use.
I quickly ruled out everything except CT, MgT1e, and T5 for a variety of reasons. The biggest ones are that they are all out of print (except GURPS, but I never liked the system) and that, quite honestly, I wasn't thrilled with the whole rebellion and virus timeline.
While I love CT, I also knew it's limitations and was using it as a baseline. So I bought the MgT core book and the T5 CD to check them out. Here is my short synopsis of them.
MgT is pretty much CT+. It builds upon what was in CT and adds to it, and the large majority of what it adds is good stuff. It uses the same setting (that I love) and felt vary familiar. There is a ton of extra materials from both Mongoose and 3PPs to allow you to go in any direction you can dream of in the Third Imperium setting, or one you create. The rules are pretty simple and straightforward to learn to get started.
From a referee standpoint, if you want to stay in the 3I setting, or something similar to it, Mongoose offers everything you need. In addition to the published books there are active communities online discussing it and creating stuff for it (here, at Mongoose, reddit, Facebook, and even Yahoo Groups). However, if you want to go beyond the 3I setting, and a 3PP hasn't published something similar to what you want to do, you may be doing a lot of trailblazing and homebrewing.
T5 on the other hand is a massive, robust, and comprehensive toolbox that will allow you to build pretty much anything you want, in any setting you want. It has tools and rules to build pretty much anything. Want to build a Gun, there is a "Maker" for that. Clones? Got you covered. New Sophonts? Can do! Vehicles? Check. Worlds? Check? Tech up to TL (I forget, but really high)... it's got it.
However, it is currently missing a robust setting, supplemental materials, and 3PP support. I use the analogy that T5 is similar to Bethesda giving you access to all the tools, widgets, and assets to build your own version of Skyrim or Fallout, with a 1 page set of directions.
EXTREMELY POWERFUL, if you want to spend the time to figure it out. But not very approachable to first timers.
When I first looked at T5 it took me about 2 hours to figure out enough about how to roll a character to give it a try, and I totally got it wrong. Then once I did figure it out, I found that the original Rogue chargen was broken. T5 can be overwhelming to most people.
So I went with MgT because it was easier to figure out and introduce to new Traveller players and had a ton of supporting material. Besides, I could easily convert my CT stuff to MgT to recycle it.