The biggest difference between Windows RT and iOS is the apps.
Let me preface this by saying that these are my own personal opinions. Also let me say that I'm not claiming that this is the only difference between the operating systems, but I do think it's one of the biggest differences (if not the biggest). And one final disclaimer: it's been a number of years since I've used an iOS device (iPhone 4 at release), so please excuse and feel free to correct anything that I miss on on the iOS front.
I don't want to talk about the number of apps available on each ecosystem or the quality of those apps. I'm not talking about "must have" apps or individual apps that one operating system has and the other doesn't. Lots of people like to say "Look at how many apps the iPad has. I can't live without app Xyz, so I won't switch unless your device has that app, and neither will anyone else." I think a lot of those issues that people bring up as advantages or disadvantages of an OS aren't solely up to the OS. Sure, the OS controls what API's the apps have access to and the companies provide certain tools to help entice and enable, but in the end, neither Apple nor Microsoft could feasibly produce hundreds of thousands of apps that are of reasonably high quality. If you want lots of apps and lots of good apps, you need outside developers creating for your platform.
But what the OS is in control of is what role an app can play as part of the overall customer experience, and that's where I see a major difference in the two OS's.
First of all, iOS has a huge reliance on apps for it to be useful. It does have some basic functionality such as web browsing, media playing, text messaging/phone/video chat, calendar, etc. But overall, if you want to get the most out of your phone, you better hit the appstore. I recall when I had my iPhone, I had at least 4 pages of apps. Contrast to my WP7, I use basically 3 apps - 2 are website replacements because I like the interface better (Weather Channel app and Woot app), and the other is Wordament. The built in functionality is good enough that I don't need a facebook app or messaging client app or a task management app or notes app. I know WP isn't Windows RT, but I think everyone can make the extrapolation.
Second, iOS apps have a very sandboxed feel. You enter the app, you do what you need to do, you leave the app. You need to do another task, you open another app, perform your other task, and leave the app. The apps sit in their little self contained boxes on the home screen waiting for you to let them know you need them, longing for a poke so they can have their 15 seconds of fame. This results in iOS being primarily an app launcher. Move to Windows RT. Apps have much deeper ties into the OS. Contracts let the apps seamlessly interact with each other. Again with my WP7, if I do a bing search for movie times, I also get related apps like fandango or flixter that can give me more reviews and ticket sales. It's no longer go to the "home" screen, launch an app, perform a task. It's now, be in the middle of a task, tie into another app for additional support or functionality. On the homescreen, apps aren't just given a small icon with a number to show, but they're given premium screen real estate where they can show content and information that is constantly up to date. Even the windows start screen gives you a feel of continuity by having 1 continuous screen for all the apps while still giving you the power to break them into groups to ease of categorizing/locating them.
It's very analogous to open floor plans that everyone obsesses over in homes these days. No one wants a walled off kitchen and living room and family room. They want to feel like they're in a spacious and open home that leaves them free to move around with ease and fluidity and that allows them to communicate with people in the next room without having to take the time to leave the room they're in, walk into the next room, say what they want to say, and return to where they came from.
So you can go on and on about how iOS has app 1, 2 and 3. Or how there are 500,000 (or whatever the current number to brag about is) apps available. Because I don't want "an app for that". I just want things to work. And if I am using an app, then I don't want to be aware that I'm using that app. Of course there will be things that require an app. I'm not saying apps aren't important or that there won't be that once in a while situation where I wish I had some app that isn't available to me. But in the long term, I'll take the connected OS with the growing marketplace over the more established app store any day of the week.