It shouldn't be that hard to trace signals through a well-designed hierarchical schematic. To be fair, I have seen some examples that broke the design down into an excessive number of sheets, which were hard to read for that reason. The key thing with hierarchical designs is that they work best when each sheet symbol is logically contained, so that relatively few signals (or groups of signals, eg bus or harness) are required to connect them.
It does take a bit of extra work to manage connections through multiple layers, and I do wish that were better in Altium. But that's really only an issue at the beginning of the project, and if you pay attention to the errors Altium reports it's not a big deal. Also harnesses make everything easier -- for example, running SPI between sheet symbols can be done with a single port/sheet entry using a harness rather than separate ports for SCK/DI/DO/CS, which also makes everything a lot tidier.