I think the biggest issue was that in PHB 1 you had he weapon focus with no requirement and works for pretty much every attack that a weapon user can do ... and then you have the spell equivalents which only apply in certain energy types and they all have different requirements. So, if you wanted a spellcaster to get the same benefit you need to either go with 13's in every stat (except for STR), and take four feats, and even then there are spells that don't get the same benefit.
It would be a lot nicer if they just went with implement focus right off the bat, then they could have made the weapon keyword/implement keyword issue clear (of course they still have other issues, like what powers/properties of a weapon will apply when using the weapon as an implement). In the paragon tier, they already had the feats for weapon specialization and energy type specialization. It would mean that characters with a mix of weapon and implement powers, like the swordmage, have to take two feats instead of one at the moment, but they still save by not needing to buy two different magic items (like a paladin/avenger that would either have to get a magic weapon that counts as a holy symbol, or need two different items, and still has to take both focus feats and both expertise feats to apply it to all/most of their powers.)
The idea of spellcasters specializing in energy was a good idea, but the biggest problem is that because of weapons that convert all attacks into a single energy type, it makes the energy specialization feats (at least some of them) so much better for weapon users, since they have to take a specific item to make all their powers do the same energy type [and they can turn it off if they face a resistant foe] while a spellcaster has to pick specific powers in order to do the same, which makes it harder to deal with resistant foes.
Hopefully they'll eventually sit down and clear up weapons as implements (and vice versa) so that it's known how they work (one example: can a flaming dagger turn every sorceror power into a fire attack?) and clarify the various feats for weapons, implements, energy types, etc.
Of course there are other confusions, like whether intelligent blademaster applied to thrown melee weapons used in for a basic ranged attack.