Even if you can't rate limit in your current release it's in the license and when you can you move people up to a higher tier. This solves the issue of charging larger customers more without them getting more value.
Unlimited number of users, files, etc should never be part of a public pricing tier. Fine for a negotiated agreement with an enterprise that has a definite period - it's a great thing to concede to close an enterprise deal and should be essentially costless. When it is in a public price list it makes larger sales much, much harder.
Keep, for example, Cloudflare in mind. They have first built their user base, and once they were used by thousands of companies, they started offering additional options, Enterprise ($2K+) accounts etc. Focus on growth first, and keep some aces in your pocket for the time your revenue will stall. This way you will be able to be innovative whenever growth is slow, and there is a possibility a competitor will show up and take your business.
I've been planning to add additional perks to the larger tiers over time though. For example, I'm now working on audit logs, and will likely limit the amount of history for the lowest plan (sort of like Slack).
On the per-user pricing, how do you think about the possibility of a company that signs up with just a few users but manages hundreds of servers through the product?