Wow, you really are unhappy, aren't you!?
2. I have to admit that I didn't really like the Temple related stuff - it was too late in the series to introduce such a big new thing, and new characters. But, as with the statue, I don't feel the need to know exactly who built it or why.. it's just something else which has been there for a long time - and if they'd been allowed more seasons, maybe we'd have seen more.
1. & 3. My interpretation is that as the protector, Jacob made up his rules*. That would have allowed him to go off island if he felt the need, but could also prevent MiB. If he truly believed that letting MiB go would be that dangerous, then he would have made the rules so that he had to stay.
* This was first referenced by MiB himself, when they were playing their board game. He actually told Jacob that one day he could make his own game, and make up his own rules. This was later confirmed by Ben, who told Hurley he believed Hurley could run things differently, and make up his own rules.
4. Is that really important to understand? You need to be a man of faith!
5. I'm not entirely sure what I think about this, but I've listening to a podcast for a while where they discuss the fact that whatever is truly needed on the island can be found.. all the way from a pregnancy test, to a lighthouse. As for the wells, who's to say they hadn't seen those? They wouldn't have been important to them, so they wouldn't have been mentioned. Although, of course, during the time travelling, Locke went down a well, which led to the 'donkey wheel'.
As for the stream, the twins hadn't seen it until they were shown by Mother, and MiB states that he'd been looking, and couldn't find it. I assume that it's something you can't see unless you're 'allowed to'.
A lot of things do seem to come down to just accepting, making your own interpretations, thinking it out etc. Not everything can have a straight forward answer. As I say, a man of science or a man of faith?