Uhh, what?

Progenitor is like the best colony ship out there. It's got good damage spreading abilities (Malice), and it's shield regen can make or break the outcome of a battle.

I always start with a Progenitor, and most people do as well.

Colony frigates suck compared to Colony Caps.  The frigate starts with 225 AM (antimatter), uses 100 AM for each jump, and needs 90 AM to colonize.   (So: 225-100-100-90=-65short).  Frigate's AM regeneration rate is about half that of Cap ships.   Frigate's regen .5, whereas Cap ship regen .85+.1 for each level, (lvl 3 Cap = 1.05 regen rate).  Frigates are very fragile compared to Cap ships (about 1/4 the hull, and basically no fire power).

Frigates usually can't colonize more than the adjoining planet, without dieing, or waiting till all militia is cleared. And then when it is safe to jump in, you usually have another long wait till enough AM is regen'ed.  Even more so, if you've already used 90 AM to colonize the prior planet. 

Therefore, Colony Caps allow you to expand much more quickly.  I believe the AI is especially subject to these disadvantages.

I disagree.  You generally get better offense on Carrier Caps, but thats about it.  Malice and Nano Disassembler are some of the most lethal abilities in the game.  Ion Bolt is also one the best interrupts for killing fleeing Caps.

I prefer a Radiance with Detonate AM; it often removes enough AM to prevent a missile barrage, as well as acting as an interrupt.  But I hear people saying: "build a Revelation" for Reverie, for a nearly non-stop interrupt.  But a Radiance is also usefull against titans, so I don't know which is best.  In either case, they both seem to die too quickly (to focus fire) to be of much help.

I'm not sure which game mode you mean here but 5v5 online I often see other caps. Marza is the most common TEC one unless they are in an eco spot. In a suicide spot I usually get a Carrier Cap as I don't need to expand much beyond the nearby asteroids anyway. The Radiance isn't as common for the Advent but some people do use it - especially as it has some nice uses late game that you mentioned. There are definitely some weaker capital ships that could use some buffs but I don't see colony frigates as any issue in this. It doesn't make much sense to me to compare a colony frigate with a colony cap - and you're not really answering the question of why should the frigate be improved at all? What is wrong with the current colonization and expansion rate? All working as intended imo.

Generally you would not just be using a colonizer in one direction only anyway. Carrier caps, Marza, Kortul, there are quite a few with better offensive abilities, but yes, some of the best abilities are on Colony Caps too. The problem with a 2nd cap ship - at least in 5v5 online type games - is your point about the cost/damage of it compared to equivalent in frigates really. Once in a comfortable position later in the game, it can work to get more out though. Or in something like 1v1 or 2v2 on larger maps where you have the time to fleet AND get 2 caps and level them a bit before large engagements. Not sharing experience would help but I don't realistically see that change ever happening.

The Marza opener isn't just about hoping you get to Lvl 6 - it has more firepower than Colony Caps and its ability to bomb out planets quicker makes it a winner in early battles over territory. I don't often play Vasari, so I'm not sure why more people don't open with Kortul - especially as you're going to be getting colony frigates anyway. Advent, like I said, Halcyon and Radiance are perfectly viable unless in Eco spot and haven't been that uncommon to see in my experience. I think it's more about people's comfort zone - Colony Cap is a safe bet so why deviate? That doesn't mean others aren't viable or have advantages themselves though. And I don't think having to use a colony frigate slows you that much in most opening positions - how far are you planning to jump with it in a 5v5 where you're only 3-4 jumps away from the enemy anyway? Plus you're going to want some to contest neutrals after the colonization phase with them too.

Radiance I am less sure about as I honestly don't think I've ever opened with one - but I have seen other good players do so from time to time - maybe a better choice as a late game addition vs Titans though I'll concede. Halcyon is honestly quite amazing though...

Shield Regen vs. Missile Barrage - its (SR) radius is pretty small - and bunching your fleet up within it is probably not the best idea in this situation.

If you micro it right it can buy you precious time to retreat your units, you definitely aren't going to be outlasting MB with it unless you actually kill the marza while shield regen is up...not good for corvettes or illums, only disciples, as they crowd together pretty well and move quickly...I'd say I have about a 30-40% success rate with it, and when I did fail it was in large part because I had either lums or I had low level shield regen (you really need level 3 or 4 to be safe)...

It certainly is not ideal, but it is possible and the prog has several other advantages that help you win in all other situations...