No, I believe everything will stay the same, but new damage type may be possible (analagous to dark, holy and chaos) and possibly we'll see armours and such with reductions to these damages. Possibly there will even be new forms of armour with Mantra-like reductions of damage rather than AL, so that you have two forms of armour available; you can have AL60 robes or AL40 robes with 25% reduction of elemental and magical damage for example, leaving you vulnerable to physical but providing some protection against armour ignoring spikes; that kind of thing.
If they follow MtG there will likely be specialised forms of damage and such with each expansion; they're on the right track with the cross-attribute skills, this is similar to the "kicker" costs and such used in some MtG cards; I could see analogues of "phasing", "shadow" and such as being possible, as well as specialised dual class skills, or skills that benefit greatly from a combination of effects (warrior attacks that do more damage if you hit a foe with a mesmer hex on them, ranger shot that deals more damage if you have a necromancer enchantment on you, Fire spells that work better if you use a ritualist spirit, earth-armours that get a synergy with protection magic and so on).
I suspect that the balance issues that MtG faced are pretty much similar to those that face GW; how do you introduce new stuff, make it fun and desirable, yet not give too much of an edge to those with the greater number of skills and such; you make the damage ranges all similar, but you open up new mechanics that aren't advantageous per se.
