This is a silly question but I am bit confused. What are the disadvantages of removing HTML tags before indexing the pages?
I can think of two good reasons.
By removing all the HTML tags you're removing all the semantics of the text.
This disadvantages any ranking algorithm - all else being equal, a page with "Tree" in a heading is more likely to be about trees than one with "tree" in the text somewhere.
You're also discarding attributes that could be used to index.
To illustrate, a link to an image of a tree might have alt text describing the tree. Discard the alt text, and your page might not show up in the search.