What is the best way to connect an MCU with a crystal and its two capacitors?
I would certainly echo the comments here saying it doesnt matter. At, for example, 32MHz, the wavelength is more than 10m, so your tiny trace will make no difference at all from a transmission line impedance perspective. The only thing that could matter, then, is the stray capacitance and inductance. At this scale, you'll be looking at 1-3pF/in, and 10-30nH/in. This means that an extra 3mm of trace makes absolutely no difference. I dont really like layout 3, but I can almost guarantee that there will be no performance difference between it and the other layouts.
As mkeith said, there is some thought that acute trace angles are bad, but I have looked at this a few times and concluded that, as far as I can tell, this is a holdover from many decades ago. If you talk to an RF engineer, they will say it doesnt matter for things under GHz, and you should maybe avoid for PCB fabrication reasons (acid trapping etc), but if you talk to a fabrication person, they will say it makes no difference for that but maybe you should look at it for RF reasons. You can google around to find more info on this if you are interested.
One thing that is important more generally though is that you add a ground plane flood, which will help your circuit in other ways.