(I am sorry if this solution has already been discussed, I cannot find them in this forum)
Currently I think there are some problems with flat damage skills not scaling well with T1, possibly worse when more tiers are introduced.
The original idea of flat damage skills is that to
1. Force (allow?) flat damage skill users to focus on stats other than DPS such as focus, cast speed, crit chance, crit damage to boost the damage.
2. Make wands and staff best (or good enough) weapon for mages, as there are usually more cast speed or caster-related bonuses on wands/staffs more than other weapons.
Therefore, to still keep the original idea of the skills, while make them scale with equipment tiers, I think one possible approach might be to make the skill damage scales with weapon level.
This will still force mages to find focus / cast speed / crit / etc. attributes on the weapons but also let the damage scales with upcoming weapon tiers.
For example, flat damage skill damage can be changed to A*B, where A is the usual amount that scales with level, and B is the about that scales with ilvl of the weapons.
The value B for weapons of ilvl 100 and below can be set to 1.0 (no change from the original), and as it might be hard to think of a formula to calculate this scale B automatically for ilvl > 100, it could be manually set for each distinct ilvl values (I think there are not much distinct values of ilvl > 100 weapon right?).
In this way, the damage could be easily made scaled with T0 T1 and any upcoming tiers. (For example, the value B for T1 weapons could be set to 1.5 or so, as dps-based skills usually gain around that much from weapon dps).
I am not sure if this is easy or hard to do by the torchlight mod system though.