I completed almost everything before the rebalances, my base2 is lower. I think your issue may be weapon choice, don't be afraid to retrofit to other weapons nor forget to use your reactor.
for base carry I went base1 optimized for damage base2 optimized for battle mult base 3 max penalty reduction + battle mult. trusting outranging the enemies + 2 deflectors to do the trick, which worked for me till 4/6 after which I just didn't have enough damage output. And now my base improvements are in the realm of years for 1&2.