As someone with something ridiculous like 4000 hours logged on NA siege, here are my thoughts:
1. DTV has murdered NA2 population, because it's at least twice the gold/XP per hour. But the siege players that play DTV mostly hate DTV, and only play it because it's populated and good XP. My proposed solution? Restrict DTV to < lvl 31, so people can use it to learn cRPG and grind through peasanthood, but not farm their high level characters.
2. It's really hard to populate NA2; no one wants to be stuck on x1 while waiting for 8 players to arrive. My proposed solution? Eliminate repairs while the population is <8.
3. The multiplier+valor system is a poor match for siege, but I get the feeling Tydeus is working on changing it (based on that "offset" debug text). Right now, the best strategy when you end up on a doomed team (i.e. the wrong team on a map that heavily favors offense or defense), is to just ignore the flag and fight on the walls for relatively easy valor (your teammates sitting idle at the flag actually bring down the average points, helping you get valor). It's pretty dumb that you get rewarded for ignoring the objectives.
4. There are still a few maps in the rotation that are ill-suited for typical NA2 populations; Burg Rabenstein and Ridoma Castle are still in the rotation as of last night, and I assume Hailes Castle is also still in. These are maps where it takes attackers a minute or more to get to the flag, which means that when the population is low, defenders have respawned 3 or more times while attackers are still running to the flag. I'm sure these maps play great on EU with 50+ people, but with <20 people on NA2 they are snoozefests that cause most players to quit. NA2 is more suited to smaller, faster-paced maps like Himmelsberg Monastery.
Ultimately, I wish that Battle and Siege would be merged into a single Conquest server. I felt that this game mode showed amazing promise, and it's a shame the devs abandoned it before it was complete. It combined the best elements of Battle and Siege, without the worst negatives, and the beta conquest map that was on the NA2 rotation for a little while was 90% there, IMHO.