As mentioned above, the setting is (mostly) separate from the system. What you probably should be asking, is what setting do you want to use?
There are, as I see it, four main "current" settings, and a number of steps or what have been called 'milleaus'.
So, in no particular order:
Setting one - The Original setting, or "CT" setting as some call it. Goes up to about 1110 or so, so just after the FFW. The Vanilla setting, if you like.
Setting two - Rebellion, where Dulior murders Strephon, and it all goes to [beeeeeeeeeep] in a handbasket.
Setting three - The Virus, where a certain well-known antivirus protection firm whose letters sound a LOT like a character from a fantasy movie from 2005, starring Emma Thompson, screwed up and let something outta the box - whoops, sorry, wrong script
![Wink ;) ;)](https://cdn.jsdelivr.net/joypixels/assets/8.0/png/unicode/64/1f609.png)
Seriously, this is the one where a computer virus somehow achieves sentience, and does a Skynet on all organics. IMNSHO, it's a lame idea, and why they released TNE (which I refused to get for that reason).
Setting four - The most optimistic of the lot thus far, and the version I prefer in my own games: "The Lorenverse". This continues the thread of the CT version, which is the original setting, no rebellion, virus, or other nonsense, the 3I continues along, Strephon as Emperor, Dulior killed in a shuttle "accident". Oops.
Aaaaaand then there are the so-called 'milleaus', where you go back along the 3I timeline, and stage the games in 'historical' settings along that timeline. (and yes, I'm completely ignoring the Empress Wave. Hey, it's MTU, I can do what I like
So, it's not (strictly) about the CT mechanism. It's about the setting. And let us not forget that you CAN bin the entire GDW setting(s) list, and "roll your own" setting (which is what my last Ref did, btw).
As to mechanisms. I prefer the MT system, as devised by DGP and published by GDW. I don't mind the MgT2e setting, but it requires the purchase of more and more rule books (what is this, WH40zillion or something?!). You can get the
ENTIRE CT and MT settings and books (less certain third party and unadopted publications) published by GDW from FFE on a couple of DVDs for a LOT less than a half dozen new rules books, frankly. Not that this is stopping me, as a lot of people still like to play the newest shiniest books on the block, but even so, the older systems are well-established, and work, for the most part. That, btw, is where 'house rules' (of which I have a few) come into play. And I still get to use whatever setting I like, if I'm refereeing the game.
So, yet again, not about the CT system, it's the setting.
Have a better day!
(Edited for spelling and clarity!)