Ok, here we go again having extensively used both. At one time, I had both in my rack
Here is my take on the Eclipse vs Ultra:
Hardware:
The Axe-fx is 2U the Eclipse 1U. Less space in the rack for eclipse more screen on the Axe-fx.
Ins and outs:
Eclipse has all balanced ins/outs. It has 2 analog ins (1/4 or XLR), 2 analog outs (1/4 and XLR), AES/BEU ins and outs, S/PDIF ins and outs, ADAT optical ins/and outs, word clock, midi in/out/thru
The Ultra has only unbalanced ins and 2 balanced outs. The Ultra has a total of 4 analog ins all unbalanced, 4 outputs (2 1/4, 2 XLR and 1/4), one set of input/outs can be used for an effects loop or seperate ins/ outs. S/PDIF ins/outs. AES/BEU out (no in), no word clock. MIDI in/out/thru
The Eclipse has a built in sample rate converter and can support multiple sample rates up to 96Khz, the Ultra can only support 48Khz.
Both have to foot pedal jacks and remote power for devices thru 7 pin MIDI.
The Eclipse has a compact flash card for storing presets
Algorithms
The 2 units use different paradigms for effects. The Ultra is guitar centric arranging things in a 12x4 matrix of blocks. Each block can contain an effect such as an amp, cab, reverb, chorus, etc. The Eclipse has a large set of predefined algorithms. Each algorithm may contain one or many effects. You can only use 2 algorithms at any given time. Turning individual effects on/off is not as intuitive or easy to do as in the axe-fx. The Eclipse is not really guitar centric.
The Eclipse, on whole, has finer granularity in its effects. This allows for great detail but at the cost of easy programming. The Eclipse is not as user friendly as the Ultra IMO, the user interface seems to be laid out more for an engineer the an average user.
Routing options are very limited on the Eclipse. The Ultra's routing possibilities are virtually endless. With 4 ins and outs adding external effects or completely seperate signals paths make for an extremely powerful tool.
Effects
The effects in general of both units are fantastic. The Ultras effects have tendency to be less colored than the Eclipse which adds that Eventide flavor to most things (not a bad thing). The with the ultra adding eq, feedback loops, advanced tabs,etc. can be used for getting more colored results.
Reverb. The Eclipse is deeper in how it can be programmed and it can get REALLY huge. The Ultra does allow for as large of a reverb w/o using a plex delay or diffuser to supplement it. That being said when you use a couple of the axe-fx blocks together , you can get marvously thick, lush verbs. The reverb are MUCH easier to program on the Axe-fx (just seleect the type of reverb and adjust a couple of parameters), the Eclipse uses more obsure terminology and take longer to craft IMO. However, you can get some superb reverb both from the presets and from taking the time to craft your own on the Eclipse.
Chorus/Flange/modulation - I love the chorus/Flange on the axe-fx, dialing it in is a relative breeze that parameter names are intuitive and get a great chorus is easy. The Eclipse has great preset chorus and you can do a lot with them. They sound great but they are a real pain to program. The flange is similar. With the addition of the zero-thru flange setting on the axe-fx, it is one of my favorite digital flangers. In general, both units have excellent modualtion effects, the eclipse is generally more granular while the axe-fx is generally much easier to dial things in. Again IMO.
The ring mod and comb filtering is much better on the Eclipse IMO
Non-linear/drive effects
When it comes to distortions/preamps/cabs etc - the Ultra stands alone there
Pitch/Harmony
The quality of the pitches goes to the Eclipse, while the Ultra is not bad (better than the TC IMO). It Eclipse tends to have a sweeter more musical sound. The Ultra has better tracking in my experience. It can even go glitch free thru simple chords. Plus you can place the pitch block any where in the signal chain and get the pitch source from either the Ultra input or the blocks input. The Eclipse can do a total of 8 voices shifted. The Ultra can only do 4.
Modifiers
You can put a modifier on just about any parameter in the Eclipse. The ultra is much more select about what you can modify. The Eclipse also allow you 3 different ways to modify something (unipolar -from base up to a point , bipolar - up and below a point, and absolute - between % point of the parameters range). The ultra only has unipolar. Both offer extensive modifying ability. The Axe-fx is easier to wrap your head around and program. The Eclipse take a bit longer to get the grasp of. The Ultra has an auto engage capability. to automatically engage a effect block w/ a foot controller sweep.
For me, it basically boils down to this. They are both pro-quality effects units. The eclipse is generally deeper with many parameter able to go to higher extremes. The Axe-fx allow for much greater routing capabilities, the abilty to craft you own effects chains instead of programmed algorithms. The Eclipse hardware (balanced ins/outs, SRC, extensive digital capabilities) fits supremely in the studio. The Axe-fx lacks some of those studio features. It can still do quite well, but again is very guitar centric. The Axe-fx has fast switching time while the Eclipse (even after the update) is very slow.
Finally, the customer service. While Eventide has fine support, Fractal is a customer driven company. They constantly listen to the users and make changes based upon that input. It is quite remarkable. Any bugs that are found are quickly squashed. Eventide is much slower to admit and correct bugs IMO. On the other hand, they generally have very few because they don't change things as often.