Yeah, I was a little disappointed by the lack of custom scales in the PitchFactor, too. It has a bit of delay between algorithms, too. It's not terrible, but is noticeable. The PF doesn't have as much of a delay as the Eclipse does, but the algorithms aren't as big and the Eclipse's architecture is getting old. However, the PF does NOT have a delay when changing intervals, keys, or modes, as long as the presets use the same algorithm. It can be true bypass and can have tails (to let the effect fade naturally). It has a kill-dry, too, so it works well in parallel loops (with or without a mixer).
Live, I just use a mixer and have several processors setup for each sound I'll need for a song. The only other way to eliminate the algorithm-change lag is to use a processor that just uses one big algorithm and turns parts of it on and off for "presets." To me, the complexity of the dedicated algorithms is worth the price of admission (e.g. mixer, multiple processors, etc.). It's not just Eventide. My Lexicons and TC Fireworx have noticeable delays, too.
I will add that the PF does more than just harmonizing. It's delays are really nice, too, and micro-pitch shift... It easily does stuff like Vai's Liberty (like the Katana demo above) and Ballerina. It is a LOT better sounding than either the G-Major or G-Major II (I have both). The PF has 4-voice harmonies, does crystals, and does Whammy style shifts. Here's a list of the modes it does support: Major, Minor, Dorian, Phrygian, Lydian, Mixolydian, Locrian, Harmonic Minor, Melodic Minor, Whole Tone, Enigmatic, Neapolitan, Hungarian.
While I'll admit that I like Eventides, I just want you to know what you'd be getting into with a PF, both the good and the bad. I like TC's stuff, too, and have owned a number of their rack processors. If the preset-lag is a deal-breaker, the PF isn't going to work for you. I wouldn't say that the G-Major does harmonizing just as well as the PF, though, but it may be more than sufficient for your needs and you get a few more types of effects. But, the PF does several effects that the TC can't do, too. Either way, both are very valid choices that have all worked for me.