I think stereo and text speed needn't be options anymore. I think the game should be in stereo if the music is famitracker and the option for surround sound if midi. I don't know who would want the text to display slow as molasses. What I don't like is when there's autotext that appears on the screen for only a couple of seconds. I'm a slow reader, and stuff like that is hard to catch. I think that the dialogue text speed shouldn't affect the time the autotext is up, if you decide to put autotext in a game. I like @Br81zad's suggestion of allowing you to scroll through the dialogue.
I think simple animations (like FF4/FF6) is fine and adds aesthetic to the game, but long, drawn out animations every time you do something gets old. At the same time, I feel like something is missing if you turn it off altogether. If it's possible, maybe have the animation for the first instance and then a shorter version for multiple instances. That would still keep it fresh for each battle but not waste as much time, and then there wouldn't be a need for an option to turn it on/off.
I like the active battle mode, personally. It keeps you on your toes. One option would be to allow the player to press select to pause the game at any time. That could help them with battles if needed. I don't think Chrono Trigger gives you the option to wait, but I might be misremembering.
I actually liked the wheel menu in SoM and SoE, because I'm a visual person and loved being able to see what I was equipping/casting/using. In a regular Final Fantasy type of menu, I would suggest having a description of what the item does at the bottom of the battle screen. I recall some games having descriptions in the Main Menu, but I don't remember if the descriptions are there during battle. I know Crystalis and a bunch of other games have a more visual menu for equipping and using items (and Mystic Quest above, I see. Forgot about that). I really enjoyed the visual options in Shining Force (the nodding and shaking head comes to mind immediately), which is also used in the Golden Sun series. Phantasy Star III also uses this visual menu in battle.
I also like in the Final Fantasies (at least 1 and 4) there's a small icon next to each item that tells you what category it is. That is immensely helpful. One alternative to the SoM wheel: I was also thinking what if you had the battle options (fight, magic, item, etc.) at the bottom of the screen and popped up an image of the weapons that can be used, item options in a window thatappears above the menu, or use the shoulder buttons to scroll through them. I don't know if I'm explaining it well. I'll draw you an example and message you. I never understood why it would take a turn for you to equip something from your inventory in FF4. You should just be able to use it right away.
A visual control config menu is also a good thing to have as a menu item.