My personal opinions, for what they're worth.
The new FF healths haven't affected my blobbing on average. It just makes me blob longer, but in optimal situations I hardly lose anything but time due to them, with the drawback of just making attacks somewhat more frustrating.
On the other hand, when they manage to make a difference, it's rather harsh. There was this one planet in early game, when I played last night, which had all these under a mk2 FF:
* mkIV Factory
* Ion Cannon (mk 2)
* Ion Cannon (mk 3)
* Orbital Mass Driver
* Black Hole Machine
* AI Eye
And the whole place had many guardians and few hundred ships. The pile of stuff was pretty much as far from the only entrance worm hole as they possibly could be. I did eventually manage to capture that place by pouring in enough ships in small dozes at a time (needed the mkIV factory), enough to mostly not stir the Eye's attention, but it took a small forever even so. If you look at the starting situation, it's pretty cruel. If I go after the FF, the other ships and ion cannons slaughter any ships I have. If I go after the ships and guardians, the ion cannons slaughter me, and at worst the Eye summons more ships. If I bring in a lot of ships to hammer the FF, the Eye summons more ships for defense as well. If any of my plans fail, I can't save the ships by retreating because of the black hole machine. And because it's the first mkIV factory I've found so far, I don't have any normal fleet ships yet that would survive the ion cannons.
Maybe I could've been able to use Raid Starships, didn't try those. It was the first Orbital Mass Driver for me, and that thing looked nasty. Figured it'd probably just chew 'em to bits before they could do any real damage.
All in all, IMO, the high mark FF's should be tough, but the lower mark FF's should be slightly weaker than the current in relation. Also, how about allowing to build a tough FF from the Zenith Traders to balance things?
The FF Bearers are also unbelievably tough. I've only played a little of 4.0 yet, but so far it's a ship I'd put on my must-have-if-at-all-possible list.
Then the MRS. A blob without MRS takes constant damage, while with MRS it can keep going pretty much indefinitely, especially with those FF Bearers. Now, looking at the price of the MRS, it doesn't quite feel like the price that saves you a few hundred ships at best. Any other thing that results in saving the life of that many ships will cost you tens of times more. So... I dunno. Anyone else feel its price isn't quite reflecting how awesome it actually is?
Still, having fun with 4.0+ a whole lot.