I agree with you that every character shouldn't be able to counter everything, but they should all be able to do their job without being easily countered by the majority of the opposition. Just about any creature/enemy can charge you and thereby threaten you 'till you die, with you being relatively useless in melee, especially at low levels.
The major issue isn't high level play, when you can countercounter with enough forethought. Early and mid-level play is the real issue with precision damage (and one that isn't relevant to the thread).
My desire to refrain from Skirmish (an ability I don't particularly care for at early/mid levels) and GISH rules sort of pidgeon holes me into volley archery, which sounds fun, but lacks damage against higher level monsters with high DR. I guess I'll have to carry a lot of different arrow types.
Tumble takes care of most of your worries...
If charged, hopefully between armor, dex, +AC from moving with skirmish, and various other defense bonuses you have keep you relatively safe. Then, on your turn make an easy Tumble DC 15 check to move up to half speed without provoking an AoO and with luck that should move you 10+ feet which is enough to reactivate your skirmish again for another Manyshot attack - or if the Travel Devotion feat was used you may be able to use Rapid Shot/Improved Rapid Shot.
Magic bow makes ammo magic so I just carried a quiver of each metal (silver, cold iron, adamantine) plus a normal quiver. Was heavy, but I didn't need much else. Also for the archer PC I played I was almost never directly attacked as there was usually a Fighter type between me and the target.
I'm not saying my way is the right or only way, I just saying for the archer I played this was very effective and dealt significant amounts of damage as I was either using Rapid Shot or Manyshot on every turn with skirmish damage. I don't know how much of the MIC you use, but there is so much in that book an archer can benefit from. Hell, just the +1d6 elemental damage weapon crystals for 3,000gp are great so you can spend your +1 enchantment bonus(es) on something better.
O'yeah, if playing an Elf PC for your archer, look into Elvencraft Bows. You're bow doubles as a staff and you threaten with it/can make alternating ranged or melee attacks with it IIRC.
There is also a 1st level spell, I don't recall the name, but the spell lets you threaten and make AoO's with a ranged weapon - get a wand with that or use the DMG rules to craft a ring with either charges/day or a permanent effect, pricey, but could be worth it.