I really miss the focus on the heroes units (cap ships). What ever happened after release im not 100% sure about, but they dont feel as important anymore.
In beta 4 the first cap ships was really important, really powerful and with a few frigats it was alot of fun. The gameplay video from beta 3 and 4 shows this.
This is because the capitals started at level 3 back then, instead of level 1. A level 1 cap stands out much less early game than a level 3. Alas, most of us older beta testers fought to the brink of death to keep the starting game the way it is, but IC felt that "losing the cap early was too hard to recover from" in agreement with a fairly loud outcry from other testers.
On the other hand, though, they added more militia around planets, so now it's possible to get a level 3-4 capital after clearing just 3 or 4 planets, so it doesn't take too long to get that feel back.
The new Empire tree, i dont like it at all, i miss all the planets/asteroid that was on there. I found it was really useful to move fleets around to colonize, conquer and explore new areas, and micro your planets.
Psst, you know you can autopin planets so that everything your scouts visit gets pinned? Or did they make it so that only the ones you own get auto-pinned? And besides, you can just pin the star and expand it. So there's several ways to get what you want on it. The new tree is more flexible than the old one, and allows players to customize it more to their tastes, instead of forcing either an "everything visible" or "only selection visible" tree as it was in beta 4.
Also they removed the ctrl+1 like grouping icons and replaced them with fleets. I dont know about anyone else but i dont see the fleet useful at all. For the ships to be really effective in fleet battles you gotta handle them yourself anyways, so i dont see the use.
You haven't played around with fleets enough

Fleets are a very nice organizational structure, and not meant to be more than it is really. It's a means of keeping your ships together, so that you don't have to constantly watch them so they don't do anything stupid. Before, you had your control groups and your light frigates would always charge forward into enemy defenses and get shredded. Now with fleets you can keep them together with your other ships without the need for a constant eye. You can set them to "local area" attack, and they'll serve as a line of defense for your fleet (which can be set to "gravity well"), so they'll never wander off to attack random targets, but always hang around and attack whatever comes close to your fleet. So just like with the empire tree, the fleet system provides a lot of extra flexibility. And the best thing about it is, you can still make your control groups and give them whatever orders you want, and after they're done they'll just fall back into fleet formation rather than be spread out everywhere in the grav well. Fleets = organization, something that pure control groups don't have.
Gaming speed, i believe 1,04 slow speed was the beta 4 normal speed. In beta 4 people took there time for a great game that took its time. Most games today are played on fast which is like any other RTS games out there. So to me Sins have become a normal RTS game with a Z axis.
The speed was a really important factor of how the game felt epic, and meant alot to the strategic aspect as well.
This is really one of the major reasons I don't play much MP. In beta we were quite content keeping it on the lower settings and having fun. But so many MP games are on everything fast now that it's just not as fun for people like us who enjoy slower paced games. Alas, the option is there still but most people prefer to play fast, so what can we do

Of course there are some directions the game went in that I don't agree with completely - like us arguing for keeping siege frigates the way they were, but IC has their own vision too, and I respect it.