Suppose we could start from scratch and create a proper system for research papers. Here is how I would envision such a system.
XML has become the standard for storing information on the internet; it gives a simple machine-readable method for creating tree structures. Academic papers have such a tree structure (Sections, subsections, theorems, proofs, etc.) that would lend it itself well to XML. Mathematical equations should also be written using XML, we already have a MathML specification for doing this.
A academic paper XML file would only have content information, not any formatting information. For this we would use XSL files, themselves XML files that describe how to format the document. You would use different XSL files depending on whether the paper is viewed on the screen or printed, and different publishers can develop their own XSL files to have consistent looking papers. LaTeX, the system used by most theoretical computer scientists, has similar capabilities but because LaTeX does not enforce any standards, changing style files often requires considerable editing.
Researchers will not have to create these XML files directly (unless they want to) but can use word processors that will save the documents according to those standards.
For citations we should just point to a unique identifier for a paper, no longer should we need to cut and paste bibliographic information. The formatting program can go online based on the identifier to get the information to create a human readable bibliography with web links if appropriate. Most publishers already use Digital Object Identifiers (DOI), we just need DOIs to point to an XML file giving bibliographic information, have DOIs for unpublished papers and have a method for DOIs to point to a later version of a paper.
The author information on academic papers are often useless (like my postal address) or out of date as academics change locations. Each academic research should get their own DOI-like number that points to an XML file giving personal and contact information and then we only need add these DOIs to the academic papers.
Most importantly we need to have enforced standards for each of these XML documents (via XML schemas). If we can truly separate the content from the formatting of documents, and make that content available in an easy machine-readable forms, not only can researchers focus more on the writing and less on the style but will also open the door to applications that we cannot even imagine today.