Some thoughts from a factions vet:
1. Unless there are over a thousand players this wouldnt be a case. Starting in factions will be incredibly easy if it was the size of the towny server. If its really that hard to get out of spawn just add a /tpr (random tp) command.
2. This is why YOU HIDE YOUR BASE. Go a thousands of blocks away from spawn and build a base underground. Try to bust into that. Big factions won't waste time on smaller factions most of the time. Getting raided in faction is a part of the game. If you don't like that go play towney. Even bigger factions get raided.
A solution to solve this:
Add "peaceful" factions. These factions cannot raid, be raided, pvp, be killed in pvp, tnt damage turned off, etc. This is a thing in the factions plugin(Unless I forgot). However though you can't just build up your faction in peaceful and you will need to apply for peaceful flags on the forums etc.
3. There will always be faction superpowers. A faction can Branch into different ones, and have protectorates. Although I'm pretty sure a faction can only have 30 people by default. Again, factions is not designed to be fair and friendly.