I keep closing your portfolio on accident because if I click on a project, the project takes over the entire window without opening a new tab or leaving a back button to click. This is bad. If someone closes your portfolio on accident like that, they might just move on to the next one in their list of applicants.
They won't help - especially if you call them "Research Papers". Your portfolio shouldn't showcase a bunch of your homework - it should showcase ONLY your best work. If you want to showcase your writing about video games, then you should start up a blog on gamasutra and start pitching articles to websites like gamecareerguide or game design aspect of the month. Labeling anything on your portfolio in a way that suggests "I had to do this for a class" is a bad idea.
1) How important are research papers and journals to a game designer portfolio? In my mind, being able to articulate the game industry and analyze a popular game's mechanics would show knowledge about games. I realize having playable games are more important, and that is what my portfolio primarily contains, but would a few papers also help?
I don't see why not. I'm partial to itch.io for hosting downloads, but you don't have to use it.
2) Right now, every game on my portfolio can be played online and most can also be played on Android. Even with this, should I also provide download links for the game executables? Is there a particular hosting service I should use for this task?
On top of "Only show your best work", I'd like to add "If you don't think it looks like the work of a senior designer, it isn't good enough to be on your portfolio yet".
3) With each piece of my portfolio I tried to both show wireframes/prototypes as well as tell a story. Is there any standard on how these entries should be constructed? Most articles I've read online have said this is a vital piece to a game portfolio and yet I could only find a couple game portfolios that did this.
The idea behind showing wireframes is to show your design process. You can do this without the wireframes.
Keep using itch.io. If you're sending someone off of your website, do so in a new tab so they don't accidentally close the tab that has your portfolio on it.
4) I currently have a few games up on itch.io and link to them. They're playable web games but the itch.io links contain downloadable executables and gameplay information. Should I continue linking to itch.io or should I instead move the web games to my server and put instructions on their portfolio page? Also, in general, should I continue having every link open a new window?
I think your portfolio currently has too much in it. You should cut anything you don't consider your best work and improve anything else until you believe it is high enough quality that a senior developer may have worked on it. Your goal isn't to simply convince HR that you know what you're doing - your goal is to convince them that you are the BEST candidate for the job.
5) Is there anything missing from my portfolio? I am working on a map and game mode for Unreal Tournament (2014) so Unreal Engine/3D Level Design is represented but is there anything else I can work on? Right now outside of Unreal Engine I plan on finishing what's in my portfolio. Hopefully the Phantasy Star Online Journal will be completed before the end of the year.
Structurally, I would move your name, your desired position, and the projects up to the very top. I don't know who you are, what kind of job you want, or what your skills are when I open your website for the first time. I have to scroll down to find out. The bio should be at the bottom if included at all. I think the video is pretty cool, but I'm not sure it's something that belongs on your portfolio. I'm pretty good at foil fencing and I've won a blue ribbon in tango at a ballroom dance competition, but neither of these are on my portfolio because they don't showcase my ability to design or develop games.
If you'd like to see an excellent example of a portfolio, check out this one: http://www.carolinedelen.com/
If you're looking to break into the mobile space, you should definitely be showcasing your programming skills as well on your portfolio. Mobile teams are usually smaller than your typical AAA team and they tend to want to hire people who can wear multiple hats. I like that you share the code for the pinball game on github, but make sure you clarify what work you did. I don't know if you worked on the code or the art for this game. I also wouldn't share the design document. Most companies won't look at your design document for the same reason they destroy unsolicited submissions without opening them - they want to avoid any risk of liability if they are working on a project remotely similar to your document. I also don't see any of the art styles from the document represented in the game.
For the resume, you're losing a lot of space to your large margins. Vertical space is expensive on the resume, and the easiest way to get more space is to shrink your margins to fit more content on the page. You lose a lot of space with the huge indent on your content. Your skills should be higher up on the page as well since they're going to be more important to HR than what school you went to. You should also include the url of your LinkedIn page on your resume and put in big bold letters at the top what job you're looking for instead of using an objective line. If the top of the resume says "Game Designer" then we can skip the objective and move on to what skills you have to offer the company.
I also wouldn't put your GPA on the resume or on LinkedIn if it isn't above 3.5. Some companies will immediately rule out your application based on that alone.