Hang on, still not sure I've got it.
First let me paint the picture I'm guessing would be the "ideal case":
Weapon users go the Weapon Focus route, getting extra damage for their preferred group (or groups) of weapon.
Implement users go the "Elemental Focus" route, getting extra damage (or other nifty bonuses) for their preferred type (or types) of damage.
That is, martial characters focus on their tool. Magical characters focus on the damage (type of damage).
As I understand it, part of the problem is that magic weapons turn your martial powers into elemental attack powers? They really should only convert the damage to elemental damage, while the power itself not counting as an elemental attack! (Yes? No?)
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Now, I can imagine this "ideal case" to be a bit restrictive for special classes, but why not first implement the above, and then override it for the special cases? (Just like all other rules work in D&D)
That is, let me take a quick stab at getting the above to work; then you can help me out by pointing to what builds and what classes break, okay?
Weapon Focus: gives +2 damage for all your powers with the Weapon keyword for a specific weapon group. The benefits of this feat does not stack with the benefits of any other "Focus" feat.
"Elemental Focus": gives a benefit for all your powers for a specific damage type, regardless of how those powers are delivered. The benefits of any one of these feats do not stack with the benefits of any other "Focus" feat.
("Elemental Focus" is my shorthand for several feats, including from PHB1 and Oncoming Storm from PHB2)
The point is that for any given attack, you can only claim a single "benefit". Keeping things balanced between characters who use "easy access" tools (weapons) and those who use "difficult access" tools (implements).
So if you have a Lightning Longsword +1, and the feats Weapon Focus (Heavy Blades), Raging Storm (PHBp200) and Oncoming Storm (PHB2p178) you can't get all three benefits for a single attack (you'd need to choose):
+2 to damage (through Weapon Focus)
+1 to damage (through Raging Storm)
+1 to attack rolls with subsequent Thunder powers (through Oncoming Storm).
Of course, I still think the regular Fighter's attacks with a Lightning Sword should not count as Lightning powers. It should remain a martial weapon attack that unlike Lightning Bolt shouldn't benefit from something like Raging Storm.
(Then feel free to have a "irregular fighter", a Swordmage perhaps, who can benefit from this, and being balanced accordingly. But that'd be a special case which the general rules wouldn't have to take into account)
Am I on the right track here? Isn't this what the discussion is about...?