In Fallout 3, The enclave wanted to rebuild the government and enforce the government by using fresh water instead of bullets.
While the AI wanted to use a FEV virus to kill all the mutants.
Are the Enclave the bad guys? Let's look at the Brotherhood they killed the enclave and then instead of trying to create a new government just gave out free water and ignored the wastelands problems.
Enclave seem to be the only good guys, why? because they wanted to rebuild rather than do nothing.