Thanks to a report from Mike i was able to fix the comment issue over the weekend. Unfortunately its something that i didn't even realize I had broke.
To explain the problem, i essentially removed the default way Drupal displays the links at the bottom of posts because i did not like the formatting. This broke the add comment link, hence not allowing you to post a comment. Its been fixed, and you should see the comment fields at the end of posts if your allowed to comment on them.
This is the style of headache I've had with trying to get a nice looking theme setup on Drupal. I Remembered i had a problem like this before, and sure enough, i had blogged about it in the past. Drupal is a complex CMS, and finding where some of the output is generated can be challenging. It does not help when Drupal's forums users seem to ignore my posts. I had started 5 threads for various problems i was having, and ended up having to solve them all myself since no one responded.
So that leaves me with a few options for the future. I can
A. Suffer though the problems with drupal and themes
B. Try and build my own theme from scratch
C. Try another CMS or Blog site all together
Sure, i could build my own CMS, i know enough PHP to do so, but i defiantly don't have enough patience to try and code all the back end features that make a CMS useful. I'm thinking ill try to do B first, now that i have a better understanding of how themes work in Drupal, and if it comes to it, find another CMS package that works better. There has to be something better now, its been a while since i first starting using Drupal.
It comes down to my wants and needs overall. I want minimalism, but not simplistic. I want smooth design, but i want to emphasis the content more than the look. And i want it without feeling like i'm somehow breaking other features.