I would agree the Evacuator is good, but besides being a decent colonizer, the Progen is really weak. The "good" combat ability of the Progen, Malice, doesn't work well against the strategic mix of abilities of other civs. The very light hull of the Progen means it is easy to kill, and Malice doesn't seem do anything unless the ships it is affecting are being damaged by some other means. Since typically ships are being killed one at a time (ie. focus fire), Malice is therefore mostly wasted anyway. Malice only shows value when illums are being used, and multiple targets have a possibility of being hit. Even then the usefulness of Malice is debatable since the period of time Malice affects a target is usually less than it takes to kill it, at least that is true in the first half of most games. Later, presumably one would have a larger fleet and make better use of it, but since ships are ordinarily targeted one by one by a player, Malice is fairly inefficient most of the time it is used. And it is catastrophically inefficient compared to other cap ship abilities of other civs.
Most Advent ships are made to be lynchpins of their fleets, more than any other race. Re: the Progen, Malice is a way to multiply damage...it doesn't do crap by itself. The really powerful ability is shield restore. It does so much to keep your fleet alive, it isn't even funny. If you cycle shield restore a couple times, your fleet can even weather a Marza Missile Barrage. Progen is not a one vs one fighting ship at all, though it is very hard to kill if the rate of damage can't crack its shield restore. Go Radiance if you want a 1v1 ship.
The way it is now, Advent is much more challenging a civ to play than TEC or Vasari for the simple reason that it has been given a poor set of abilities. The pathing and speed of the Advent ships seems more clumsy than other ships also, since I have chased Marzas across several gravity wells with disciples and for some reason the Marza moved faster and jumped faster than disciples (andno, the disciples were targeted on the path endpoint of the Marza, not the Marza itself, so they were not getting tied up within the grav well firing instead of jumping. And no, they were not group jumping either, they just seem to hang up on the grav well edge more than the Marza did.)
Advent requires more micro management and careful grouping of your fleet, but the abilities are powerful. Cobalts are much faster than a Marza, but they probably were getting hung up trying to align for jump. You had either 2 problems -- 1) They were in a fleet and trying to stay in formation to jump. 2) They were all trying to go for the closest edge of the gravwell to make the needed jump, and were getting in each others way to align for jump. Sometimes you have to manually coax them to give them some margin before giving the jump order, so they all turn and jump at once. For these reasons it is challenging for a group of ships to pursue a single fleeing ship. Cobalts are definately faster though with a max speed of 800 and acceleration of 200. Capitals have a max speed of 525 and acceleration of 100.