spoilers inevitable
An interesting thread. I think that anyone who has already beaten the game twice or more times is in a good position to decide for themselves exactly how to approach their next game, and preserve the most important element; fun. Here are a few of the things I did, some of which relate to your original comments:
1. No stealing from stores at all. I just pretend its not possible and for the first time i have had to spend thousands of gold on spells (three casters in my current party) which previously would have just been lifted. Money management in my current game is fun again as in my first play-through, when i didnt know about stacking potions of thievery and stealing ad lib.
2. No ranged weapons at all. Apart from using fire arrows to kill off the trolls at the keep, I have stuck to this and it is highly recommended. I dont allow melfs or energy blades either.
3. No bags for items. Scroll cases and gem bags are allowed, but the other 'silly' bags are not permitted in my current game. I presume the items in my characters' inventory are already in implied backpacks (and not clutched permanently in their arms, while still wielding swords....) This is easier for experienced players because they know which items can safely be left behind.
This also removes the temptation to recharge things ilegally.
4. Battle preparation. You raise a good point here, in that many of the battles occur somewhat 'by surprise' so it disturbs the integrity of the game if you fully buff up first. However, there are lots of situations where one can see the battles coming by having an invisible scout (something i used even in my first play-through) go ahead disarming traps and checking out the terrain and enemies. Here I think buffing and prepping is fine. Fun and personal taste is the key here: getting into the Mencar Pebblecrusher fight totally unprepared at low levels is exciting and rewarding when you win, but after the tenth reload you might decide it would be more fun to summon a couple and buff a little first.
5. Character stats and abilities/ proficiencies. I like your point about the extra stats being a 'reward' for getting through every corner of BG1 first. I treat the matter differently however, and do as I please with shadowkeeper to alter the characters to my tastes. This is not cheese - this is my reward for completing BG2/ ToB 3 times! When i took mazzy for the first time i noticed she was grand master in bows, in my game with no ranged weapons! So I changed it to swords

I gave Nalia 19 int because it makes no difference to the game except that she can scribe the spells i want her to scribe without relying on potions of genius - it saves a couple of mouse clicks here and there. Would I make a character with 25 in every stat? No - because i want to have fun.
6. Extra items from mods. Many of these are far too overpowered and cheesy for my tastes, and spoil the fun of the game if I use them (most of the weapons in 'item-upgrade' for example). Some are fine with me. I was so impressed with Sanchudoku when i first had it that i took it through the game, and made sure I got it in my next game. This time though I accept that it is overpowered and I have not installed the mad kensai mod as a result. On the other hand, I have 'cheated' a bit this time, in a way that makes the game more fun for me: I have altered Nalia's De'Arnise Signet Ring to give it some extra abilities. Nothing too cheesy, but lets just say its a lot better than Edwin's necklace thing
7. Battle cheese. The battles are the core of the enjoyment of the game; seeing my characters succeed and progress as a result remains rewarding to this day, so I fully agree - no cheese allowed, nor wanted as it spoils the fun. On my virgin play-through, I am sure I used the off-screen cloudkill tactic having come up with it myself at the time. That's fine, but as a veteran now i feel obliged to 'wade in' to most stuff. Even if it means running away/ micro-management as a result.
8. Wands. I have never used these too much but have no complaints about them. Generally they are not as powerful as the 'real' spells, but as an experienced player i now know that they are less resistable in some circumstances (eg cloudkill). As for recharging them for free, I can only think that relates to selling them and stealing them back, which would not be possible in my game with no stealing from stores. Wand of resurrection could be construed as cheesy for its healing properties - I pretend it is only useable by my cleric for this purpose, and feel it is fair for him to heal mid-battle with it.
9. Duplicate items on simuls / projects. I dont see a problem here personally. Project Image is a very powerful spell and this is one of the reasons why. Mages are clever and can see the potential of their spells - all power to them.
10. Mods in general. Most of them have their faults, but overall i love them, and applaud the work that has gone into their design. If it adds to the game, is bug-free, and doesnt upset game integrity, I use it. Otherwise i dont. Some experimentation is necessary of course, but examples such as the lich in the underdark, improved bodhi, the extra fights in the docks district and so on are such welcome additions and add fun (and challenge) to the game. Any overpowered items can be left un-installed or ignored in game to suit personal tastes. If you do the lich in the docks unprepared and un-buffed you will probably feel you deserve the cloak of balduran.
11. How are we helping the less fortunate, trudging around in here?