The fundamental philosophical difference between EOS and IOTA
EOS is right now about to launch their main chain, and IOTA is about to announce more details about their Qubic project with smart contracts, oracles and computing resources trading.
Both EOS and IOTA are promising free instant transactions, and IOTA will also add smart contracts. But unlike for example Cardano, Ethereum, Lisk and so on, you can't compare IOTA with EOS directly.
EOS is a platform with a lot of work put into governance. You can think of EOS like an integrated operating system.
IOTA on the other hand is a set of open permissionless standards. Any product or organization can use an IOTA standard and really pick and choose which IOTA standard they will use. You can think of IOTA as file systems, small Unix-programs or standards like TCP/IP. You can build your organization, product or technology on top of IOTA just like Linux Distributions take many different projects and put them together in one integrated product.
EOS is aiming to be a very open libertarian society, but it is not truly permissionless. If you aren't behaving, the EOS community will kick you out and they might change the rules. If you are using IOTA "wrong", you can just keep on doing that, but the standard is made so that it will just not benefit you to misbehave. Example: Right now there is a coordinator which is basically the IOTA Foundation saying which transactions are valid. No one has to listen to the coordinator, but if you don't, probably no one will validate your transactions unless you are very trustworthy.
Of course EOS is truly permissionless in the way that you can download the code and run your own EOS chain that works just like you want regardless of what the community thinks of it. You can also create and run your own IOTA Tangle, and the project Oyster has actually done that for their product. But a separate Tangle is sort of like having a private Internet - less useful. You want to be connected to the main Tangle, which is exactly what Oyster is aiming to do in the future.
As there are many possible ways to run a blockchain like EOS, and you can have different constitutions about how to solve conflicts and fund development. But IOTA's Tangle is just a "simple" protocol that is agnostic about how your organization and technology works. Just as you use TCP/IP from MacOS, Windows or Linux, you can use IOTA's Tangle from a sensor, a browser, an EOS smart contract or anything.