I have not yet made the switch to TA but I do not imagine the starbase dynamics have changed too drastically from DA that my comments would be without some small merit.
I make extensive use of all three types of starbase when playing and find that, used correctly, they are incredibly powerful. So I do not think the benefit is underrated.
However I am not making a 'you're doing it wrong' statement. I bashed my head up against the wall of starbases for a long time before I started figuring things out. I'm amazingly stubborn that way - and without such a disposition I wonder how players are meant to figure these things out. Without an intimate understanding of how to get the most of starbases the benefit to the player is limited, construction is clumsy and defence is difficult.
I can see why you are making the argument for simplification of construction, but the current implementation does have its benefits. I thought I would run through several of the things I do in case some find it helpful, some may be obvious but its possible to miss the obvious and i'd like to be thorough.
* 2 levels of miniturization provides the tiny hull enough space (20) to mount a construction module. This is the cheapest way to build as the outlay for a cargo hull is larger and only provides access to a great deal of space you wont be using. Generally speaking I will add nothing else (indeed it will be a long time before you even have the option of adding to a tiny hull design - I use cargo for specialist builds) unless its important eg: engines to grab that galatic resource faster.
As a result of this, and the fact the early game is unsuited to anything but the most rudimentary starbase construction, I do not invest much into starbases before this ship is available.
* Even though the tiny hull is a 'military' grade hull you will pay no upkeep (as per cargo designs). This is an incredibly beneficial aspect to the current starbase construction model as it allows you to amass an armarda of construction ships and dispatch them to where they need to be or upgrade a starbase with just the right module when you need it.
Even if you have no current plans for positioning a starbase it never hurts to have some spares rattling around in your pocket. Theres nothing quite like sneaking 20+ builders into the centre of another races territory and creating a 'fully armed and operational battle station' on the eve of hostilities. Sometimes the AI reactions are quite amusing too.
* Planets with a starport and one or two factories are perfect for producing a steady stream of builder units. You do not need to make every production planet a wasteland of factories - adding a starport and a factory to an econ or research world can work wonders at freeing up production planets to larger projects.
* The biggest source of stress for me when I was wrestling with starbases was the feeling of waste when I did not micro manage every single last building unit. Refer back to my earlier point on upkeep - you pay nothing for idle units. Then reflect on what is in fact being wasted. If you hold back constructing a starbase until you need it you save any starbase maintenence costs.
When you eliminate the feeling of waste a lot of the stress deflates out of starbases - it also allows you to feel a lot more comfortable using rally points. A few missed turns while a group of builders form is not such a big deal anymore. In addition moving builders around in groups by hand tends to avoid constant popup windows of starbase upgrades while you try to remember where is and what prorities starbase 3245 had and indeed if you even own a starbase 3245 - maybe you got some other galatic emperors mail by mistake.
Need should be at all times your guiding star on where you proritize building (this is also in my mind the driving force behind the entire concept of the game).
* Defence. This is a big one. My biggest misconception early on was that starbases are great impregnable fortresses. Its a mistake to think that and many have pointed out how vulnerable starbases become as the game progresses.
So my next mistake, in thinking that since starbases are not fortresses was thinking that they were non combatants that needed to be protected at all times by ships. Since the ships are there we don't need to bother with modules right? Well thats only half right - they do need to be protected at all times. But they have all those guns and missiles and bombs and ballistic cow launchers for a reason.
Its better to think of arming starbases as a last line of defence. Theres nothing more frustrating to see a 20+ module starbase explode because a very determined teenage Dregin fired a hand disruptor out of the window of his space charger while doing laps around the starbase.
This brings up another point of stress on starbases. Because you now have vulnerable fixed position targets in your empire you now find yourself scrolling out to tactical view each turn and squinting at all the little icons, sacrificing chickens and performing auguaries to determine if your starbases are under threat. Because the only thing more frustrating that a teenage Drengin blowing up your starbase is the 63rd Battlefleet, Terra Invictus, Scourge of Thalan, Bane of the Dark Yor, protectors of the sector watching from guard mode with buckets of popcorn.
Do something! you scream. Then you open up your save games, scream again then quit to desktop muttering angrily about starbases. It doesnt have to be that way. Arm your starbases to a capacity that they can deal with 'leaks' to borrow terminology from Tower Defence type games - but that connection is natural.
Your fleets should be intercepting concentrated enemy forces prior to engagement with starbases. You should be thankful the AI was gracious enough to dash the brains out of the wounded survivors on the rock that is your starbase. It should look something a little like a Tower Defence.
* More Defence. Yes I have not finished making points on this. How do we go about defending starbases in a stress free but effective manner? I tend to group my starbases together. If a cluster of planets is juicy enough to benefit from a factory laden economy starbase its juicy enough for two factory laden economy starbases. This is most likely why theres a cap on starbases per sector (though it can be incredibly benefitial when a sector boundary intersects a sweet spot).
Well that battlestations mk 1 isnt going to hold off more than one teenage Drengin at a time - you need a fleet. Defensive fleets in my mind don't need no stinkin engines - the best way to make sure somebody stays around to protect the flag in a capture the flag game is to cut off their legs.
The extra benefit of this is they now have more room for everything else. They need weapons to make the bad guys go kaboom and defences to make sure they are still around to make the next wave of bad guys go kaboom - because having to constantly resupply defensive fleets will have a significant impact on your ability to project force into enemy territory.
Worried about mobility? Well thats why you also throw down a military starbase to secure the sector. -enemy ship speed and +ship speed compensate handily for the lack of engines, as do passive advances in propulsion technology - with the added benefit of speeding up those old tiny hulled builders.
Extra extra benefit? The AI will respect your impressive attack+defence total and think twice before declaring war (which allows you the luxary of subverting his populations with influence starbases). Hand in hand with this is the benefit ship assist bonuses from military starbases count towards your military rating - try it to see for yourself.
This leads me in to my favourite defensive ship size - the tiny hull. A lot of people write this hull size off as obselete by the mid game due to low hp and insufficient space to overcome this vulnerability. The benefit from the military starbase is greatest with the tiny hull. The benefit of a +1 ship attack becomes +15 ship attack when you have 15 fighters in the fleet to benefit.
I have personally experienced some incredible defensive victories with fleets of fighters taking down fleets of battleships/dreadnoughts without taking a scratch - but that comes from my emphasis on playing the good alignment and maxmising defence. I am certain that evil players could find the firepower amplification useful.
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Well im starting to ramble now so I'll end this post here (and I did not intend to write this much 0.o) I do have more thoughts on the subject but what I really wanted to get across is that the current implementation of starbases is quite good - just really really inaccessable unless you bash your head against the wall figuring it out - it also may or may not blend well with differing playstyles - obviously it works okay with mine.
Hope that helped