I never answered the OP:
I like the idea of base attack bonuses as opposed to hit matrices/THAC0.
The AC values in BECM really don't mean anything. They're simply column labels on a chart. Change 'em to whatever you want. If you like AC to equal target number, change 9 through 2 to 10 through 17 and you're golden. "To hit" bonuses with new levels are pretty easy to figure out from the charts.
And I'd sort of like to up the thieving skills a tad to make thieves a bit more viable (or maybe add some discretionary points, a la 2e?)
Make sure you're not penalizing the thief for using his skills. Failure at a skill does not mean something bad happens to the thief. For example, a failed Move Silently check does not mean he failed to move quietly. He still has his normal chance to surprise. He simply doesn't have an increased chance to surprise. Same goes for failed find/remove trap rolls, pick pocket rolls, and move silently rolls. The only thief skill where per se something bad happens to him when the roll is failed is Climb Walls.
Let him use his skills all the times. They should be more like fighter attack rolls and less like m-u spells. Also, don't let other classes do what the thieves' skills do. In other words, if you're simply going to allow a fighter to bash the lock in with his war hammer, why bother making the thief roll to open locks? Let the thief do his job.
And I know we'll be using my old BECMI favourite - death at -10, with those in the negatives losing 1d3 HP a round (and cures do NOT restore you to 1 instantly).
I actually had a group request that I stop using the -10 rule. True story. They wanted 0 = dead. Personally, I prefer the 1e rule that any character brought to -4 in a single blow is dead. If you're brought to 0 to -3 you're incapacitated and lose a hp per round, dying at -10. And of course, if you go to -6 or worse, you have some sort of scar or lose a limb or some such other coolness.
1e/2e's basic secondary skills system could be fun to play with.
I'm not fond of tacked on skill systems in D&D. Generally, if a player says his character has something in his background, I allow. If he was raised by fisherman, he knows how to fish and knows a bit about boats, etc. If I were to use a skill system, I'd go to the 1e DMG and use the secondary skills (which is a slightly more formal version of my previous sentence) instead of the Survival Guide/2e style NWPs or the RC style non-weapon skills.
My brother wants to use 3e's Saving Throw mechanic as opposed to the BECMI standard.
See my comments in previous posts. I'd suggest as a compromise using the BECM saves for things that fall explicitly within the BECM categories and then a Fort/Will/Reflex type thing for stuff that does not. Maybe it makes things overly complicated, but I think it might be fun. Or you could go the complete opposite direction and try a Swords & Wizardry/Tunnels & Trolls single value save system.
Some extra purchaseable commodoties might be a fun idea (read as: stuff to do with your money that's not related to your castle).
More stuff to buy is always cool. Aaron Oliver (aka Mr. Reaper from Dragonsfoot) has a
Rules Cyclopedia Errata and Companion which has a much expanded equipment list. In general, it's an incredible document, much of which I disagree with, but is an incredible labor of love for the BECM rules with tons of ideas and things to think about.
Any other ideas? Suggestions?
Let the players come up with their own spells per the spell research rules from an early level. Make expert hirelings like sages, animal trainers, and alchemists available to players, too. Use the charisma, henchman, stronghold, and follower rules to encourage the players to cement close ties to some npcs, to become more attached to the campaign world.
Most of all, have fun.