Akin to such ships as Homeworld's motherships.
Not really. The HW1/2 mothership's best defense was to not get into combat in the first place; in HW2 a mothership might have had the gunnery to defend itself against, say, a minor bomber strike, but against most forces a mothership would require external support. A mothership's main advantages lay in the fact that your unit production facilities were not tied down anywhere, but was a mobile installation in itself.
In HW:Cataclysm, there was the armed mothership. But it wasn't carried over to HW2.
My point in bringing that up was that the OP was being far too ambiguous.
I like the flagship idea, it makes a lot more sense than the current flagships have no added benefit situation, it reminds me of the Enterprises being the flagship of the Federation and other similar ships. Needs some fine tuning, but it looks promising.
And here's where I point out that a "flagship" has little meaning, because a flagship is simply a vessel with a flag officer, i.e. an admiral, aboard. Ironically, this makes the USS Enterprise of ST fame most emphatically not a flagship; rarely, if ever, did it carry a flag officer. In a similar vein of irony, the Endgame future-USS Voyager was indeed a flagship, as future-Janeway was a Vice Admiral, making her a flag officer*.
As a result, a "flagship" makes sense contextually as a vessel that the flag officer chooses as his command center. In Sins, this means that the highest-level capital ship (i.e., capital with the most experienced crew) is the "flagship". Though, somewhat oddly, if there are two vessels of equal level, then neither will be flagship (this is mostly apparent in long SP games with multiple high-level or level-10 capital ships).
*Off-topic, but I truly fail to see how Janeway would have been promoted to being a flag officer considering the numerous examples of her rank incompetence seen throughout ST:VOY. First and foremost being that she could have used timed explosives on the Caretaker's Array, allowing it to send USS Voyager&crew home, and subsequently being destroyed.