It’s a good start but you need to study more about typography and other design rules.
Background for your theme is really bad and distracting. You should remove it. Theme on that link has good typography, spacing and colors. Try to compare it with your theme’s details.
Modernizr like any other script is not necessary at all. That’s your choice which scripts you add for theme.
If you’re from cheap country then yes it is great career choice. If you’re from rich country then you have more opportunities to make good career choices with or without web development. But you should always do what you like the most.
If it is one page theme and you have scrollbar as navigation then it must use script for scrolling. Don’t deregister Wordpress scripts that is not good practice. Try to delete all registered external scripts from your functions file and add only modernizr to see what will happen then start to add one by one external script to see which one will cause problem.
For isotope you need to have defined max-width for gallery images in style.css, it needs to be the same as width of column for that image (you’re probably using some css grid system).
For modernizr – add it in head of your theme and try to change order of preload scripts in your “scripts.js” file, add script for navigation on top of it, maybe it will help because it looks like some js conflict with navigation js ( I assume you use js for navigation). And use noconflict jscripts in WordPress.
I would use less saturated yellow color if it is color for text background, and not so tiny font for top headline. Also rounded rectangles look outdated, make it squared or just a little rounded.
Margins are not good. Padding in black parts is too big and margins for top headlines are too big.
Maybe someone complained to support about theme’s features and they reviewed it again and found issues.
View more button probably means button with “view more” text and function. As a link to blog post from blog post preview on homepage. If you have something that looks like that on homepage you need to describe it more accurate in your documentation how that works.
I think it’s spacing issue, especially for big headlines and typography. Second example looks better.