While I absolutely agree with the comp aspect and think that's probably the biggest point, I want to add that management skill is also a huge factor. I've seen a lot of startups (YC and otherwise) fail to grow the team well because the founders are good hackers but not good managers. In a large company your manager has a manager who will help guide and review them, and you can switch teams without risking your current compensation and benefits or your vesting table.
At a startup there simply isn't room to move around without taking on more significant risks and at least waiting for your first equity cliff, and honestly many startup founders I've met don't have great managements skills, or the drive to learn them. There's also simply a matter of personalities, sometimes people just don't get along with their managers and/or teammates, but the fact that you have to switch companies and re-interview again vs being able to apply to your skip-level to switch teams is a significant difference.
Some ideas of concrete options to fix these:
* Shorter cliffs, even Google has a 2 month rsu cliff now, and I think Facebook is similar
* Maybe a hiring pool, again, similar to Facebook or Google where you pick your team after you "pass" your interviews, allow you to really work with different startups and feel out what it's like. I could see YC setting up a similar program where companies can choose to share an interview pipeline and let candidates talk to different startups after passing an agreed-upon bar for the pool. This is similar to https://www.workatastartup.com/, but to not have to formally do a technical interview for every single startup would be a huge help.
* Some way to try out/transfer between startups who allow it would be awesome. Similar to Facebook's bootcamp, if there was a way to still get paid, maybe a simplified consulting agreement that YC can help broker among a few startups for a month or so while a candidate explores what it's really like to work with each startup would be really helpful.
* Management training for founders, and a standardized way to review founder's management skills. If founder's were held accountable for their management skills and rated across one of these shared pools where their ratings were available to prospective employees, they would be much more incentive to improve their skills.