Definitely consider the Eventide Eclipse. It's what I went with. There are some advantages and some disadvantages, but IMHO it's one of the best effects processors in it's class.
It contains all of Eventides signature algorithms found in the TimeFactor and ModFactor pedals. It DOESN'T contain the signature PitchFactor or Space algorithms, but it can do pitchshifting and very similar effects to the Space pedal. There's definitely options to program your own effects that are very close to Space and PitchFactor but it's very different how you achieve that sound. There's quite a few algorithms available from others who have done the legwork of the programming, but it's very advanced function.
On top of those, there's a plethora of other sounds. It DOES have some amp modeling now, but most seem to believe the Eclipse falls well short of other emulators such as AxeII, etc., but it's incredible with the effects and blows away AxeII and most others for effects.
It does best when wired to your effects loop in parallel at +4db setting on the amp, which the MTS amps support (not all amps have this option, some are limited to -10db), fully "wet" with your signal from the amp. I really feel that the quality of the effects in Eclipse are second to none for the available multi-effects processors in the class.
Pros:
1.) ModFactor ($399.00) and TimeFactor ($399.00) algorithms, + wealth of other sounds
2.) GREAT sounding effects!
3.) 1U rack space
4.) With time/skill, incredibly flexible with programming your own sounds
Cons:
1.) Cost. If you hurry, you can pick up a brand new one on Amazon right now for 15% off, or $1,695.75 which is the cheapest I've been able to find a brand new factory A-stock. If you're patient you can find a used one for ~$1k on evilbay etc.
2.) 2-channel processing, only 2 effects at once. Still not bad for a 1U rack unit, but you can obviously have 3+ simultaneous effects with pedals, and AxeII supports a ton simultaneously also.
3.) Complex. MUST read the manual, and takes a lot of getting used to and getting your presets all set. Not for faint of heart/short of time if you want to get your money's worth out of it. You can get VERY deep into programming this unit!
4.) Switching between presets (for different effects) is slower compared to pedals (which are almost instantaneous). Especially guys who gig often prefer pedals (AxeII is also lightening-quick) as you can really fly through your effects. The time it takes the unit to load the algorithm has really improved with the latest sw, but still slower than some options out there. For studio use, this isn't really a factor, but for live gig, it's not as quick/easy to toggle through effects, and you're somewhat limited to the number of presets you can toggle through with a controller without having to go to the console.
I guess the big things are, for it's class, it's hard to beat the quality of the effects. The programming possibilites are a plus and a minus. Many who play out opt to compromise on sound quality for easier/quicker toggling between effects, and changing settings on the fly (i.e. the turn of a knob on a pedal vs. going into the menu on the console).
Lot's of interesting discussions out there:
http://www.thegearpage.net/board/showthread.php?t=851341