This was required for custom webpart from where I could change the font size, font colors etc.

I could solve it by two ways:

1. Make new css files and store them in the kentico stylesheets.
The web part stores the users settings in the session/cookie.
change GetCss.aspx.cs to load the class from session/cokie.
Drawback: kentico updates will overwrite the GetCss.aspx.cs and you need several css files

2. Add this line as the first line in your css stylesheet in the kentico
@import url('~/CSS/DynamicStyle.aspx');
Add this file in the filesystem with code like as follows:
body
{
background-color: <%= GetFontBGColor() %> !important;
font-size: <%= GetFontSize() %> !important;
}
Here GetFontBGColor and GetFontSize are c# functions on that page retrieving user settings from session/cookie.

Hope this helps.