Ok... I lost a map... because I failed to tame the bats fast enough... Why!?! they should have just thrusted you into the next map.
The only I have, honestly, is with the timed losses - which is one of the reasons I generally like swamplings. Many of the levels don't have a time thing, and I didn't even notice most of the others that did. The exceptions are the bat training level and the "failed assassination" level - the second mostly because I spent forever fighting guys.
1) Seperate Autosaves, Replays, and saves (heck seperate them by campaigns as well). In fact this is THE suggestion I give. The rest of my suggestions is really just "add stuff even if your not going to use it".
I don't understand what you mean?
2) Editing program for editing that isn't the map editor.
I don't think this exists for any game, honestly. But I do know Wesnoth has its own exceptionally easy scripting language for building campaigns, and there are several campaigns that exist solely walk you through how to build your own campaign I haven't played them myself, so I don't know if they are any good).
I also noticed that thieves are quite terrible... They get double damage but I've had units that can do their own damage output with actual hp to back themselves up.
The great part about a thief is its high defenses, high damage (when backstabbing), and decent hp and movement across varied terrain. Also, they are one of the few chaotic human units, and occasionally the only one you have access to. This means that they deal 25% more damage while the rest of your army is dealing 25% less. And when they level up once, they get skirmisher. I've used thieves to complete a couple missions by completely ignoring the enemy units (or distracting them with cannon foddder) while my thieves slip around the sides and kill the enemy leader.
Lets compare a thief vs. a spearman. Spearman is 7-3 at 36hp, thief is 4-3 at 24. The thief usually has a 20-30% defense bonus over a spearman, putting them about equal at survivability, but making the thief a much riskier proposition. However, lets take damage output at night. Spearman do 5-15 damage. Thieves do 6-18, assuming you aren't backstabbing, at which point they do 9-27. Despite being about the same price, thieves can deal twice the amount of damage a spearman can if you've got a good awareness of situational management. At higher levels, they also have skirmisher, a nice ranged attack, and poison as well. They are still a niche unit, and best used in pairs or groups of three, but they certainly have a place.
I still sort of dislike its ongoing nature and the fact that you never know where to level up (usually I go with what still allows you to advance but you never know where a trap is)
I still don't know what you mean by this. You level up wherever you happen to be when you get enough experience (noting that you gain experience for combats equal to the level of the enemy, and additional experience for killing the enemy, amount depending on level). Unless you mean you don't know which upgrade to take... and thats situational. Still, the upgrade screen shows all the important aspects of your options (health, attacks, special abilities, neutral/chaotic/lawful) so I don't see why it would be difficult to pick the one that best fills the niche you need.
Assuming the second interpretation is correct, I'll go a bit more into that. Generally, in single player campaigns its best to go with units that can gain another level, as higher levels are generally better. However, there are a few exceptions! First, higher level units have a higher upkeep! (upkeep is equal to level). Second, some units have special abilities that make them a lot more useful (for example, I always go with Pillagers of Goblin Knights in mainline games, even though goblin knights can gain another level, because a ranged Slow attack is incredibly useful. I also almost always go white mage because healing is awesome, and its hard to get a unit all the way to Archmage. Unless I've already got plenty of slowing units or healing units, of course, in which case I'll go the other route for diversity.
Finally, there's the leadership bonus to keep in mind. If you have an army with several strong leadership characters, it is often better to have lower level units that can be boosted by the skill. The skill boosts damage by 25% times the level difference, so if you have a lv3 leader (not uncommon), a lv3 unit will get NO bonus, while a lv2 unit will deal 25% more damage, a lv1 50%, and a lv0 75%. Usually, the higher level units are still a bit better - but they are less expendable, cost more, often end up with fewer special abilities than the short branches, and with leadership the damage increase is often not worth it.