Why, i believe the Enclave aren't bad, but instead good.
In FO2, the Enclave were isolated on their rig since a couple of months before the great war, it is now 2241, meaning they've been on their rig for 164 years. If you spend a week in your house without collecting intel from outside, you won't know what's happening, you mix that with 164 years of isolation and brain washing of the Enclave are the saviour propaganda, you will believe what you're told. Change the house to a rig with 1000 other people, you got yourself an army ready at your command, just like the U.S Army. When they emerged, sure they were a little mean, kidnapping Arroyo and Vault 13 but i can think of a few bad things the government before them did, maybe the forced military occupation of Canada or the fact that the U.S always thought they were the leaders of the world. Sure then you will seem bad. All they wanted to do was make a U.S were there was white picket fences and pies cooling on the window cill. So they set to work to make their dreams come to fruition. Just like when China invaded Alaska, the U.S army/government wanted them gone, so they used genocide to get rid or them, vice versa with the chinese. They got to Navarro and sent out patrols to keep people out, by shooting them, just like Area 51's area or Pine Gap in Australia, they'll shoot you if you get to close. When they got to mariposa, they didn't harm anyone, just a few grumpy mutants, like the so called good brotherhood, they shoot mutants on sight. They got the samples and wanted to make it work, so they tested it on some guinea pigs, just like the U.S government and the scientists at Big MT. So in general sense, besides trying to fulfil their dreams, which everyone does in the wasteland, they in their eyes thought they were doing nothing wrong. Just like the U.S government/army/scientists before the war. So before you go blaming the Enclave for killing, think, they were carrying on a tradition, just like you would at a wedding, by not letting the groom see the bride until showtime.
In FO3, the Enclave were doing as they were doing in 2241, because you must remember, the 2274 Enclave are direct descendants of the 2241 Enclave, and the 2241 Enclave are direct descendants of the Government/Army. When they emerged, they made outposts and protected them like the Enclave did to Navarro. They shot any and all because they were following orders, just like the U.S army was. When they took project purity, they only harmed one person, james got a lot of people killed, Colonel Autumn only shot Anna Holt as a warning, like the outcasts do, who are the brotherhood's brothers who are also descended from the U.S army. They took project purity because they wanted a base on the mainland, just like Navarro, they were following orders. When the Lone Wanderer showed up, thats when the FEV came into the pic, Autumn refused to kill the people of the wasteland, he instead wanted to control the water thus controlling the people and the land. He would then use the might of the Enclave to re build the world. Colonel Autumn was the good guy, Eden, who was a robot was the only bad guy who knew better. Even Autumn wanted to destroy Eden. But in the end, of course they were destroyed by the "Good Guy" brotherhood because they didn't like the Enclave. If the BOS had of listened, they could've worked together and make the wasteland great, but they didn't. The satellite array, Adams air force base were just outposts so they could communicate and re build their strength but of course the snake brotherhood ruined it. The Enclave shot at people coming in their base because they didn't want them in there. When you speak to Paladin Bael, he tells you he doesn't want you in the Citadel. I'm sure he would shoot if you tried to get in.
SO that's why i believe the Enclave weren't bad people, but instead people who were carrying on traditions and practices that the old U.S government did back before the war.
Ciao (chow) People