1. You'll have better integration between foot controller and processor in the G-System.
When you call up a preset on the G-Major, by default, lights on the GC Pro won't indicate which effect blocks are On or Off. If a block is already on, like Delay, the first time you step on your Delay CC pedal, the GC Pro will send an "On" message to the G-Major, which will be ignored and the delay will stay On. The second time you press it, things are "lined up" and now the Off message will be sent and the effect will turn off. You get used to this, though, and pre-press important CC pedals before songs to get things "lined up".
2. You'll have pedal loop options with the G-System. If you have some pedals you want to keep in your setup, this gives you multiple true-bypass loops.
3. You can route some effects pre-input and some effects in your effects loop with the G-System. It's a lot of cables, but gives you the flexibility. With a G-Major or G-Force, all of the effects will be in your effects loop, so sounds like wah and other modulation stuff may not sound as good to you.
4. G-System also does amp channel switching, as does the G-Major. Only the G-Force does not.
The only advantages of the G-Major/GC Pro setup are:
1. A lower price.
2. Ability to easily control multiple MIDI-controllable rack items.
If you only plan to have one effects processor in your rack under MIDI control, I'd go with the G-System over the other options from TC Electronic right now... unless you love intelligent pitch shifting and harmonizing. The G-FORCE does a great job of this. The G-Force also provides the most detailed programming such as re-arranging effects block order, etc... but you may not need this if you're a pretty typical effects user just in search of high-quality sounds.
Below is a review we published on the G-System when it first came out. It has had a few updates since then that make it more reliable and added a few more features:
http://www.musicplayers.com/reviews/guitar_bass/2006/0106_tcelectronicgsys.php
Scott