Don't let Commish mode "scare" you. It was put in the game for that purpose, so you can edit/customize your league. Use it.
As for your league layout, there's a 1000 ways to play and set up leagues. It comes down to personal preference. Should you use the DH or not? That's entirely up to you. Some like it, some don't. Same for minors, some like full fledged setup, some like to keep it simple.
Since you're still "learning", I would recommend a small league of maybe 12 teams, or the 16 you suggested. Think about what you want your league to be, how you want it to unfold and create history. Set things up the way you like to play, that way you'll keep your interest in the league a lot longer.
Don't do things simply because that's the way they are irl. That's the beauty of OOTP - customization. Create a world that you'd like to see, not one (real life) that you've already seen.
