- Looking at your spec you're more inline with a custom Theme then you are with a Plugin. Plugin is to modify existing functionality that works into a theme, a custom theme is what changes the look and feel of the website.
I would prefer a plugin because then I can convert any page, no matter what theme I'm using, to do the thing I described. Wouldn't that be a desirable thing? It's something I would really put to use on multiple websites and pages. Please let me know if I'm overlooking something.
-superboyac
Except you're asking the plugin to style the page for you or am I missing something. Your example built the entire page (removed menus, changed header/footer). I guess it boils down to exactly what do you need. Themes can do most everything a plugin can do and provide the look and feel for a site.
- File Upload: You should use the Media Manager that comes with Wordpress. I wouldn't recommending disconnecting any part from Wordpress as it would make interacting, from a code standpoint, more difficult
This is something I do intentionally. I upload all my files into a simple folder. It's very easy for me. I can use an ftp server and just drop files in. I strongly prefer it this way. I don't really want to upload through the browser, and click around whatever internal galleries wordpress does in the admin section. This is one area where I am really old school: I like having direct access to my files and folders...it means I have ultimate control. I don't feel this should make coding any more difficult because all the plugins and stuff I've done so far work very easily with the folder addresses that I use to link to whatever I need. When it comes to the posts and pages, I don't like the gui. I prefer to do everything and see all the codes and shortcodes. The most I would ask for is a button where some parameters are entered, and it spits out the shortcode onto the post. But again, if I'm overlooking something please let me know. I struggle sometimes with understanding the usage of page templates vs. plugins vs widgets.
-superboyac
The reason for using the Media Manager is the file information is stored in the Wordpress database and available for use by standard Wordpress methods to interact with the files. I guess you could build a plugin to do bulk uploads but not really sure why you would want that - Media Manager supports bulk uploads. FTP makes it available via the file system but then Wordpress has no knowledge of the files.
Not sure you need Widgets to start. For simplicity think of a Widget as a self-contained block of rendered information pulled from some data source. Widgets can be placed within defined areas that are pre-established within a theme - typically sidebars, header or footer areas.
You need to drop the old-school way and get used to that you're building something on an existing framework. Fight the framework and you create a nightmare for yourself. Work with the Wordpress ways and things are much more flexible. With a low budget you should develop what Wordpress doesn't provide. Go back later and improve standard functionality when the budget is there. Most, if not all, Wordpress developers would want to create something that works with the Wordpress best practices and not go old-school

Just my opinion, others may disagree.
fwiw: I've developed a plugin that supports widgets, shortcodes, custom post types, custom settings and more.