One would think that colony ships are so powerful because (flavor wise) they hold the future of your race, and (mechanically) they're usually the first cap ship people build. Free colonizer with a body to boot?  Sounds good to me. Now on the TEC Colony ship getting the short end of the Col Cap stick, it has Ion Bolt. Indeed the duration is EXTREMELY short but it if manually used on important targets, it comes in handy quite well. My only complaint is that it has a very brief (but fair) duration. Comparing this to The Evac's ND and the Progenitor's Malice, it does seem some what nuetered. But also realize that Target Uplink is more useful then it seems as the extra range and acuracy can help take out annoying fighters and moving targets. So really the Colony ships don't need to be debuffed so much as they need to balance out more. Because in an FFA between the three I'm sure the Evacuator would win, Progenitor would come in second and the Akkon would lose quickly.

Colony captials, however, are the slowest of all the capital ships. You also need to consider the fact that battleship capitals don't stay level 1 for very long if they are frequently in combat. At max level, they carry 2 squadrons themselves, and the colony caps carry 3. At that point, the battleship caps have more Hull and Shield points, have a significantly higher DPS, and generally can hold their own better than the colony capitals. Although the Egg's Disassembler does kill capitals easily, outside of that ability, its damage figures, in short, really really suck, even with a 15% damage bonus from culture.

Check your mitigation figures: all ships start with 15% and frigates max out at 57%, capitals at 65% at level 1, increasing by 1.111% per level to a maximum of 75% (Advent ships can gain another 10% from culture and research).

Oh, and FYI: Ion Bolt used on a Subverter cancels the effects of Distortion Field on your ships... just make sure you hit the first Subverter that used it on a group of ships (the second to use DF on the same group of ships really does nothing).

Targeting Uplink... well, with a 15% bonus to chance to hit with a 100% accuracy anyway... it makes zero difference except for flak. However, it can offset the penalty incurred in asteroid fields (Erratic Debris ability causes all ships to have 20% lower accuracy) and the effects of the Rapture's Vertigo (30% penalty to accuracy). The real benefit of the Uplink is the extra 20% range in order to get the first shot off with Javelis LRM frigs. With research and an Akkan with max Uplink, the LRFs can gain an extra 32% range.

Basically when you ships are mvoving and firing at ships that are also moving and firing there's a percent chance to hit, Target uplink greatly increases that chance to hit making everything much easier to destroy.

Eh, I've seen some of my ships shoot while closing in at close range, unless I was seeing things.

I would tend to agree with the OP.  The Evacuator and the Progen are extremely powerful combat ships in addition to being able to colonize.  It is really hard to not choose these ships as your first capital.  The Akkan is probably where it should be in overall power / utility.

Also, the colony caps ARE slower, but not much.  In the first couple patches, they were slower than they are now, and it was very noticeable.  LRF's were also faster, so in short, it was extremely easy to hunt down colony caps.  Now it isn't that noticeable.

I don't think this is the case. Actually I'm pretty sure ships always hit, even when moving.