In my opinion Ulthwe players are some of the most dubious, BO ridden excuses for players in all the community. With that being said I've played Matt's Ulthwe quite a bit and agree with a lot of what he's saying. As to your points...
1) 50 points to replace a guardian with a Farseer unit and go up to 1+ initiative is fine I think. Given that I haven't seen them played that often I'd be reluctant to up their cost further without some reports.
2) Reducing them to 2+ would effectively eliminate the need for a separate formation. You could just include a Guaridan-to-Farseer upgrade for the standard guardian formation and leave it at that. I don't think that's necessary though because I haven't run into the Auto Triple Retain of Doom (+2) at all. Plenty of triple retains though...
3) The SR5 is the hardest pill to swallow for me. Especially as the only downside is a 1:2 (as opposed to 1:3) core:support ratio. I think points could probably be adjusted in some areas (the formations you're most likely to activate first in turn 2-4), but whether it would be enough to justify going to 1:3 I don't know. I'd hate to turn the army into a Guardian/Aspect/Ranger/War Walker/Night Spinner pop-corn bag, which I think would be possible at 1:3. You might have to increase the number of base units in some of the support formations. I like 1:2 and think you can build some good lists inspite of it.
So in conclusion, I guess I haven't run in to these scary things on paper in a game at all.

Given that Matt puts forward a pretty competitive list build and game I don't think they're much of an issue.
Some spit balling:
1) Drop Heavy Weapon platforms and give Guardians (call them Guardian Defenders?) and/or Black Guardians a Scatter laser shot for every two units (like IG). Defenders have to take a heavy weapon platform nowadays. This also might help mitigate a 25 point bump for the guardians at SR5 as they'll have 4 scatter laser shots at full strength and won't have to worry about platform placement for suppression.
2) Add Storm Guardians (CC5+/FF5+MW or IC maybe to represent the fusion guns or Flamer) as I'm sad no other list has them.
3) Make the Mounted Guardian/Black Guardian options 6 stands and three Wave Serpents. I think 350/400 is a lot of points for a core unit in this list given the 1:2 ratio. 250/300 might see them taken more, or 275/325 if activations soar too high.