Setting and story should always take precedence over the rules, but that's not an excuse for bad rules.

The way I'd phrase it, solid rules give you the freedom to ignore them when they're not necessary, while weak rules leave you with the challenge of fixing them when they are necessary. Former is always more preferable.

I completely agree.

Picking and choosing rules is definitely easier than having to make entire new ones up out of scratch. 2nd edition AD&D had 3 different optional initiative systems, and I've never heard it referred to as a rules heavy game. But even of those 3 systems, every gaming group seemed to have their own way of handling initiative. That doesn't mean it would have been acceptable to not include initiative in the book at all!