2/ Definately room for improvement. There has to be a balance between Cata and MoP launch difficulty. If anything they should remove the 'heroic' tag and make Challenge Modes more relievent.
3/ 99% agreed. They were very briefly useful for buying rings and trinkets to boost item levels to get into LFR.
4/ Agreed, though its similar to old catch up mechanisms as well. Having better JP/VP alternatives would help - I honestly think you should be able to buy some LFR items with VP (much like you could buy T10 in Wrath), just with a high VP pricetag.
5/ It wasn't as bad as people made out - the real problem was with the Golden Lotus. Very silly gating mechanic that slowed down all over rep grinds to the point of them being mostly pointless by the time you unlocked them. And double locking the best enchantments behind Golden Lotus and Shado-Pan/Celestials was really crappy. And to a lesser extent the superior Feasts were a bit of a bugger to unlock quickly (though you could use individual food to bypass this). Otherwise it was mostly optional.