No Lucid, I *do* understand what you're saying. You're just way over-estimating the effect.
Your argument only effects skills that:
1. you know beforehand the precise value that you want that skill to be at. (ex: I have a pillow and need exactly 122 1hb)
AND
2. you have no intention of raising that skill in the mid to long term. because if you do want them higher in the future, you're going to need to pump more points in anyway.
I personally have a total of one skill that falls under this category. My nano skills, while maybe I need precisely 846 MC for my current best nano, will need to be raised in the future. The fact that I'll need to raise this anyway soon means that I'm really getting no long-term (and when it comes to balancing, long term is key) IP advantage. My evades, run speed, body dev: if I have spare IP they go here. Nanoprog, MC, nanopool: maxed. The only conceivable skill that falls under your concerns is my 1hb to wield a pillow. Let's see, I learned 1hb at level 100 or so. So I would save the attribute-contribution of levels 101-152. That's actually not too much when it comes down to it.
So the only way my IP allocation would differ given an IP wipe would be that I'd put 20 points or so less into 1hb, a skill that is only at 140 points or so anyway, so the IP cost per raise is tiny even though it's blue.
Do you see what I mean? I'm sure it's different for everyone, but it's not a major problem. Maybe it would effect profs like soldiers more, but aren't soldiers too always wanting to raise their core combat skills? Doesnt a soldier always want a higher burst or a higher FA in the mid-to-long term?
Snarf!