As a multi-startup veteran (without much to show for it but a few scars), the biggest issue is how opaque ownership percentages are. The current SillyCon Valley game is to give 5-6 digit option grants - so it seems like you're getting a lot - when there are 10-12 figure shares outstanding - and it can be impossible to find out that last figure.
Another complaint is the legalese of grants, which is usually waaay over the top, so you end up spending a lot on lawyers to translate the terms. The grants should be in "plain English" - most of the terms are pretty simple, once you clear away the legalese.
And another big deal is the little things that you might overlook, e.g., is there an acceleration clause if the startup gets bought out (very possible in this age of acquihires), or what happens if the startup actually IPOs: can you sell on the open market, or only back to the investors (which can limit your profit) ?
Also, on the topic of acquihires, if your startup gets bought out and you're a key employee, then your options may not mean anything, cuz you can -and should! - negotiate whatever you can get when the deal goes down. So it may be better to position yourself as a key contributor, than to get hung up about options.