If you want helpful advice on transitioning from gc2 to gc3, I would recommend reading this thread.
edit: I quickly reread my suggestions on the thread, since it is many months old and there have been some important patches since:
early colonizing: Not quite as important anymore, but if you end up with half the number of worlds your ai opponents have, you should figure out way to colonize more worlds.
Economy wheel and coercion: Contrary to what was suggested in said thread, coercion now sets in as soon as you stray from 33%/33%/33% distribution of manufacturing/research/wealth. 40/40/20 is still quite good I think.
Here at turn 111, which to me is fairly short in terms of a game, I was declared war on by the Krynn and immediately hit with huge capital ships with 1200 hps, 59 mass damage, and some ridiculous shield protection level (I forget but like 60).
I would be happy if they did this on my modded genius difficulty. If your beginner difficulty opponent does this there is something wrong.
Maybe you got confused by the interface, could you give us a screenshot?