1) The Africa scene makes more sense, and since that is the linchpin of the movie, that is the part that I thought was most important to restore.
2) Clark Kent, reporter. His investigation into the Batman shows why Superman has a beef with Bats.
3) Lex killing Batman victims in jail. Goes with #2.
4) Lois Lane, reporter. She figured out Lex was behind it by investigating wheel chair guy. With help from STAR labs looking into the bullet and discovering the wheel chair was lead-lined. Just behind #1 in order of importance imo.
1 and 4 are the ones that I think the theatrical cut really shouldn't have done without as they establish major plot points.
Some of the other stuff-Superman helping in the aftermath of the bombing, Steppenwolf, Lex going to Arkham are cool, but not as important.
Interesting. Just IMO, none of those actually moved the plot in a way where things wouldn't have otherwise.
1-Batman fears Superman due to the massive destruction in MoS, so he preps for the fight. (Everything Lex does in his plan pushes the issue, but is not needed plot-wise or character-wise.)
2-Lex kidnaps (a) Martha and forces Superman to confront Batman.
3-Big fight over misunderstandings, make nice when heroes discover mom's share a name.
4-Heroes unite to fight doomsday.
5-Lex goes to jail.
You can remove Lois from the movie and nothing changes.
You can remove the Africa plot and nothing changes.
Also, a lot of this relies on a) the world's greatest detective being duped on multiple levels and b) Superman being unwilling to talk to Batman like a "human being." (He says one sentence at the beginning of the big confrontation and then throws Batman down the street.)
I watched the extended version hoping some of the flaws would be addressed, but as you lay out, it just expands on a few plot elements.
Legitimately glad some people loved the movie and I don't think it is as awful as some make it out to be - but for me it didn't treat the characters as thinking beings and instead as chess pieces being moved around the board in service of plot.