1.) Javascript , AJAX can definiately affect your sites performance. However, it really depends on the application and how it is coded. For example, a bad coded infinite loop or almost infintie loop can slow not just the load time but the user's browser. In the other hand, if you are using third party's javascript code, depending on their load and how slow it loads, will also affect your performance. For this, I recommend somehow, placing there codes at the bottom of your page, so it loads last not affecting your original content.
2.) Maybe, maybe not. Really hard to tell without more information.
3.) People tend to stray away from FLASH mainly due to the fact that it is not SEO friendly. Search engine crawlers cannot read the contents of a flash embed where as AJAX content can be read.