Ahh heck, you can upgrade anything on the Ion XE because all upgrades are reasonably cheap to get hold of. best place to look to get upgrades is probably at Warped where they have a dedicated tech centre for it.
http://www.paintball-equipment-online.co.uk/index.php?cPath=39
I owned an Ion XE as my first gun so i'll run through the upgrades I would have gotten in order;
1)Q-lock feedneck - easier attachment and detachment of your loader when your putting it away and putting it back together again
2)Upgraded ASA [2 parts] - you need to buy a dovetail mount FIRST before buying a ASA with a on/off makes it a hell lot easier to put your tank on and take it off and is a simple safety feature for making your gun safe.
3) Upgraded trigger - the stock plastic trigger never satisified me, there are a hell of alot of triggers out there so the choice is yours
4) QEV Diaphram - makes the air move through the internals of your gun more efficently (I have never had one, but I have heard of others saying its an essential)
5) Upgrade the electronic Board - seriously, the settings that you can achieve with the stock board is rubbish, you need to be able to set your board to a ramp of some sort, or 3 burst for woodsball.
6) Paint - is time to get som serious training done about now, get out there and buy paint, shoot fools and learn how to win.
7)Better Eyes - Lots of cool looking laser eyes out there, take your pic!
8) High efficiency bolt - makes your gun shoot more with less air
9) Upgrade the High Pressure reg - CP Regulators seem to be the good choice with people, smaller and lighter then the stock regulator, easier to adjust the veolicity if you forget to bring that spanner. Should make the air run smoother into your gun
10) Grips/bodykits and anything else is cosmetic
Hope this helps. As you can see thats alot of upgrades for a gun, I'v listed all of them inn order, but not all of them are nessacary.