I thought most of the difference between rebel and loyalist were too high in the research tree,

Having talked about two star bases in the gravity well, I was surprised to find it as a 10th level research item. When you can build the titan at a level 4 research item this is a little late in the game.

i.e. have to expand quickly and early to make use of the turtle feature they described later in the game.

I would like to see the divergent technologies to be available earlier please.

Agreed. It wasn't until mid-late game that I actually realized that I was was having a different experience with loyalists then with rebels. And I was a sad panda. 

Yes, that would indeed be nice.

I completely agree. Truce Among Rogues is, in my opinion, by far the most potent new ability. It is the reason why I always go Rebel. I rush for it and obtain a significant advantage early in the game.

This is why I asked (in a separate post) to move *some* of the Loyalist research down the tech tree. Where Rebels seem to shine in the early game, Loyalists need to wait until the late game. (2 star bases for example.)

I wouldn't exaggerate in boosting the Loyalists' early game potential, however.

I think things work out pretty well the way they are. With the Rebels gaining the upper hand in the early game because of Truce Among Rogues, the Loyalist are forced to dig in against a superior fleet. Digging in is what Loyalists are supposed to do, so, good.

They do need some help in effectively digging in in the early game, however. Which is why I'd move one or two Loyalist defence researches down the tech tree. (Also to simply provide the Loyalist with defining characteristics in the early game.)

Back to Truce Among Rogues. When I first figured out the advantage it could get you (getting a lot of planets very quickly), I thought to myself: yeah, this is overpowered. They need to fix this. I have given it some more thought however, and think it might be fine the way it is.

1. I very much like the ability itself. It is innovative and we've seen nothing quite like it. It is what characterises the Rebels most. Taking it out of the game would be a shame.

2. Moving it up on the tech tree would make it quite useless. I have always felt Pirates can do the most damage in the early game, so a late game alliance with them would not be a priority. An alliance with other neutral factions is even more useless in the late game. Chances are they will be wiped out by then.

3. Rushing for Truce Among Rogues is not always easy. It has some serious disadvantages. Focusing on Civilian Labs means postponed access to critical early game military technology, such as repair platforms and Javelis Frigates. Also, expanding quickly is a costly business that hinders military expansion and even comes with the risk of over-expansion. (Bleeding cash and/or poor defences at newly gained planets, vulnerable to attack.) Ironically, rushing for TAR means an aggressive race like the Rebels is not very aggressive in the early game.

4. If you manage a successful rush for TAR, you need to make the economic advantage work for you before too long. Before your Loyalist enemy's defences become to strong, before he gets his superior Titan (which I feel needs some down tuning, but that is a different discussion), or before he catches up with you in general.

5. The early game vulnerability that comes with a rush for TAR as well as the race against the clock that follows it, provides a Rebel player with the feeling of being in a certain underdog position. Which is, of course, exactly right for a Rebel. I realise the Loyalist player might feel the same way when he is being outnumbered, but if he digs in properly (partially thanks to Loyalist research), he should feel safe. And the Rebel would have to challenge the Loyalist('s defences). Which once again feels about right.

You could make the argument that the Loyalist's Titan IS their early-mid game advantage

Yesterday i ran with my sole Ankylon at lvl6 into 8 enemy capships and it was going to fail hard. I was not keeping attention on what exactly is happening the whole time, but when i zoomed in, the Ankylon had half of the hull gone. So perhaps it is not as overpowered. 

Could it have had something to do with a specific ability? Like "abilities disabled" on Akylon?

Or is it possible that the regenerative ability was cooling down? I've seen the Ankylon's HP go up from low to (near) full HP several times in one battle.

I don't want to question your story, it's just that I've seen and read about a lot of situations in which the Ankylon proved to be ridiculously powerful.