This is not a familiar problem; a lot of what they have done with familiars is actually fairly understandable, and allows for a lot of tricks. The problem is that combat stealth is totally broken. Try stealthing on a ledge, shooting an arrow at foes, then hiding again as you end the turn. The enemy will do the same thing - just stand around and wait to die. This has been reported multiple times already.
Yup, spotting/perception and line of site have major problems in general.
I still think they should have made familiars somewhat autonomous entities, not ongoing "spell effects".