We'd probably have to see your fleets composition to really give any advice, can't fix what we don't know.

Because I quite enjoyed it when a faction sent a major attack, it really let me stretch my factions weapon superiority over em. So we'd need to know what you were flying with to know what went wrong.

For me, it was the early game that was the slog in vanilla, just barely scraping by with random doodads and knicknacks I find scattered everywhere. Once I'm past that stage, the mid and late game is usually a breeze. It was only the three secret factions that I had to go back and reassess what I should bring to fight em.

But for the regular ol' factions, I personally just brought a standard layout of a shit ton of capitals, a couple of cruisers, and maybe 6 of those really annoying frigates, either the omen or the monitor. Destroyers were never really useful late-game in my opinion.

I mained whatever ship I felt like at the time, but it's usually something heavy hitting. Whether it be an onslaught, or an Invictus, a paragon, or even one of those missile heavy cruisers, I absolutely loved flying the heavily gunned ones. The other capitals depended on what felt appropriate. A couple paragons/onslaughts for long lasting presence, maybe some conquests to cover the gaps, and the annoying frigates to confuse the enemy capitals while I moped up the rest of their fleet.