1. Claiming a rule makes a target, but then fails to make that target, ought to be a runtime fatal error in the makefile. I can hardly even guess at how much time this one change alone would have saved people.
2. String concatenation as the fundamental composition method is a cute hack for the 1970s... no sarcasm, it really is... but there's better known ways to make "templates" nowadays. It's hard to debug template-based code, it's hard to build a non-trivial system without templates.
3. Debugging makefiles is made much more difficult than necessary by make's default expansion of every target to about 30 different extensions for specific C-based tools (many of which nobody uses anymore), so make -d output is really hard to use. Technically once you learn to read the output it tends to have all the details you need to figure out what's going wrong, but it is simply buried in piles of files that have never and will never be found in my project.
4. The distinction between runtime variables and template-time variables is really difficult and annoying.
5. I have read the description of what INTERMEDIATE does at least a dozen times and I still don't really get it. I'm pretty sure it's basically a hack on the fact the underlying model isn't rich enough to do what people want.
6. Sort of related to 2, but the only datatype being strings makes a lot of things harder than it needs to be.
7. Make really needs a debugger so I can step through the build, see the final expansions of templates and commands, etc. It's a great example of a place where printf debugging can be very difficult to make work, but it's your only choice.
That said, I'd sort of like "a fixed-up make" myself, but there's an effect I wish I had a name for where new techs that are merely improvements on an old one almost never succeed, as if they are overshadowed by the original. Make++ is probably impossible to get anybody to buy in to, so if you don't want make you pretty much have to make something substantially different just to get people to look at you at all.
Also, obviously, many of the preceding comments still apply to a lot of other build tools, too.