I like the idea of two branches (pardon the pun) of bow technology, one being crossbows for higher hit, only once per turn fire, and bows for not as much damage but a much better rate of fire. 

To be fair, though, a crossbow IS a development from the bow, it's considerably more complex to build a crossbow than to build a longbow.  Here is my idea for the new technology tree:

Archery
   Unlocks:  Early Crossbows (technology for research)
   Unlocks:  Bow Ammuntion (technology for research)
   Unlocks:  Longbows (technology for research)
   Unlocks:  Archery Range (Building, allows creation of bows and ammuntion?)

Longbows (technology)
   Unlocks:  Longbow (weapon)
   Unlocks:  Composite bows (technology for research)

Composite Bows (technology)
   Unlocks:  Composite Shortbow (stonger shortbow)
   Unlocks:  Composite Longbow (stronger longbow)
   Unlocks:  Volley Fire (technology for research)

Volley Fire (technology)
   Unlocks:  trained bowmen who all attack in a single volley (increases accuracy, ends bowmen turn)

Bow Ammunition (technology)
   Unlocks:  War Arrows (equipment, increases bow damage)
   Unlocks:  Advanced Bow Ammunition

Advanced Bow Ammunition (technology)
   Unlocks:  Fire arrows (adds fire damage to bows, damage bonus)
   Unlocks:  Pile Arrows (damage bonus/reduces effectiveness of heavy armor)

Early Crossbows (technology)
   Unlocks:  Light Crossbow (weapon)
   Unlocks:  Improved Crossbows (technology for research)
   Unlocks:  Crossbow Ammuntion (technology for research)

Improved Crossbows
   Unlocks:  Crossbow (weapon)
   Unlocks:  Heavy Crossbows (technology for research)

Advanced Crossbows (technology)
   Unlocks:  Heavy Crossbow (weapon)
   Unlocks:  Repeating Crossbow (clip fed, same rate of fire as a longbow, damage as a crossbow)
   Unlocks:  Ballista (Technology for research)

Ballista
   Unlocks:  Ballista (seige weapon, giant crossbow that basically shoots spears, good for dragons)

Crossbow Ammuntion (technology)
   Unlocks:  Barbed crossbow bolts (increses damage)

Advanced Crossbow Ammuntion (technology)
   Unlocks:  Crossbow quarrels (increases damage, accuracy)

I like the idea of quivers being an equipped/manufactured item. Would also like to see archers possibly getting additional options, such as flaming arrows, poison arrows, and diseased arrows.

Since people are raging about archery being OP, then let's make shields useful again - units with a shield either have a flat damage resistance from arrows, or a percent chance (perhaps based on their defense or the shield in general) to take zero damage from one arrow. That is, if I have a unit of 10 shielded soldiers vs. 10 archers, each soldier will roll 1-100, and whichever falls within the percent basically ignores that arrow.

If that seems like too much, then give shields the default "Cover" ability. Whenever the unit does not move they gain 50% arrow resistance, which decreases by 25% per tile moved. Thus, archers can still effectively thin enemy ranks, but shielded units would more easily be engaged by magic or by melee units.

Will also point out that archers were a major factor in most combats, because they could easily thin the ranks of enemy armies to the point of making enemies route.

EDIT: Ishantil's idea I like, too.

With units only carrying limited ammo supplies, bigger quivers would be another useful research item.

The Monty Haul Quiver. =P

Actually, limited ammo would offer some more choices, too. Blow all your ammo on long range shots while retreating results in you taking minimum damage for the longest time but it's the most inefficient use of ammo. It would become more effective to shield the archers with a blocking unit and fire at mid to short ranges...

Making distance (and maybe height) a factor and including obstructions (which could include units, even friendly ones), would greatly help in making archery not overpowered. In this regard Age of Wonders: Shadow Magic does well, and it makes possitioning troops way more important than most other games. It also shows the modifiers (height, range, and obstructions) for your attack and the path the projectile will take / what it may hit instead of the intended target. Also, for meaningful diffrences in range weapons there needs to be a max range.

Making shields good against arrows would also be a good thing, especially if you could get compareable armor / shields by the time you get bows.

Well, I doubt we will ever get system as good as in AoW in the EWoM, that requires substantial engine improvements. But adding some variety with different damage/range/rate would be good enough start, I believe.

On a sidenote, your comment made me remember that we also need some once-per-combat ranged weapons like javelins, which should be equipped along with some other primary weapon by melee units.

The roman pilum. They didn't lug those around for show. =P

Made me think of David Drake's "Foreign Legions".  Carthago delenda est! Mwahaha!

A lot of good ideas here.  Having a sheild/cover mechanic for obstalces and shields is a great idea.  Tower shields and long pikes in phalanx formations!

I like the idea of javelins, pilums, slings, and whatever else.  Currently ammunition isn't in the game as a mechanic.  Although you could probably adapt the mana mechanic to use it for ammunnition. 

The different trinkets can help. you get an additional 4 for at from rings etc.

Yah, but I think relying on jewelry too much reduces the system to a grey soup where you pick the Cool Jewely Set Nr. 2 plus one generic weapon - which is made into a super weapon by the jewelry.

That's not very stylish. To me, jewelry should be more along the lines of "charms and amulets".
Not a source of raw attack power or armor class but rather "soft" stats.
Faster healing, luck in avoiding blows (dodge), faster recovery of endurance or mana, better luck in hitting the enemy (possible in 1.1 where to-hit and damage will be separated).

Sure, +1 Attack or +1 Defense rings were probably the easiest to create but should that be more important than making magical items mysterious and subtle?

That a magical sword hits harder - yeah, I'll buy that. But a ring...?
(well, maybe if the ring is very very big and heavy...)

In the current system (1.09), late game armor makes archers pretty lame.  However, archers can improve their hits, in late game, by adding crystal produced equipment.  Its only a +2 to attack, but it helps.