I don't think they both need to be into one skill... they just need to be worth investing in, none of thise 1%/2% per level crap

Yeah, this sounds right. I don't see any real point in splitting the skills. It's actually probably better for balance if they keep them separate.
I think the idea behind those abilities should be that for a warrior who mostly wears Physical armor, you give them a couple pieces of magical armor, then put points into +Magic armor to give it a boost to useful levels. Meanwhile, they won't invest much into the +Physical armor ability, because they get enough from their equipment. The opposite should be true for mages.
What if the bonuses worked more like this:
[x] Armor
Level 1: +25 [x] armor, + 5% [x] armor
Level 2: +20 [x] armor, + 5% [x] armor
Level 3: +15 [x] armor, + 5% [x] armor
Level 4: +10 [x] armor, + 5% [x] armor
Level 5: +05 [x] armor, + 5% [x] armor
======================================
Total : + 75 [x] armor + 25% [x] armor
At low character levels, the flat bonus gives you a useful amount of armor when the percentage is underwhelming, then at higher levels, the percentage becomes the most useful part when the flat bonus seems small.