Can someone elaborate on why (big) games like Fusion Fall (by Cartoon network), Tiger Woods PGA Tour (by EA) load their Unity game in separate browser window instead of the same window or a new tab? Is it because of the performance or any other problem like Unity plugin crashing etc. If you were to run a website based mainly on Unity, what is the best way to display it? Will it be better off being run as a part of the website like these Flash banners/websites or will it be better to have a separate window popping out of your website to display Unity Content.
If you want the elaborated answers to their decisions, it would be best to contact the web developers of the sites in question.
The reasons may be performance issues, but what type would be related moreso to the site and/or game in question.
The decision was most likely a choice of their web design and a wise one at that. If the Unity plugin is not able to be integrated easily into the main site because of Flash or some other reason, why would you take the user away from the main site (by retargetting the current window or a tab or whatever) just to play the game? Also, by compartmentalizing the Unity web app away from the main site, if anything were to go awry with the Unity-specific portion of the site, it would be easier to isolate the problem and make changes to just that part without having to make changes to the whole of the site.
Even if your site is based mainly on Unity, while there should be less need to re-direct the user, as part of good design, it may still be in your best interests to do so because the plugin can incur overhead. Overhead is best avoided whenever possible to accomodate slower connections, computers, etc.
Is it better to have it integrated or separated? Better is fairly subjective to your site, game, design, tastes, etc.