That's not such a big deal since you can obviously change the font. For a long time there were lots of text fonts but very few math fonts, and those math fonts that did exist would either have some symbols from Computer Modern or wouldn't have a suitably similar text font. But now there are a fair number of choices. Personally I like mathpazo (with Palatino for text) but I've found people used to Computer Modern can find this a bit much of a radical departure. (Edit: I've found a more conservative choice is Times for text and Utopia (MathDesign) for math.)
TeX does have a few small typesetting niggles. For example, if you set f(x)g(y) with normal small brackets around the x but large brackets around the y (because it's really a displayed fraction) then you'll find g is miles away from its argument but right next to f's argument. (I'll avoid opening the can of worms about what the root cause is here, but it's very clearly wrong in this case.) This is actually not that big a deal either - there are lots of problems like this but they're all fairly minor and small in number compared to the huge number of things typeset correctly. The only problem comes when people refuse to correct things because they assume that if TeX typesets it that way then that must be correct by definition.
TeX is like a programmable pocket calculator from the 1970s, way ahead of it's time but today it's something that conspires with Word, Google Docs, and other dull tools to suck out the oxygen for sharp tools.