You can represent these things any way you like in XML - that's the whole point of XML. For example you could use <subscript>i</subscript> or <index>i</index>. Then your stylesheet controls how this is translated into a concrete rendition in HTML, XSL-FO, or whatever you are using as a display format.
However, rather than designing your own XML vocabulary, it's always better to use one that already exists, and I would have thought the best approach for you is to use the MathML vocabulary. The advantage of this is that you will be able to take advantage of existing software for authoring or displaying MathML. See http://www.w3.org/Math/
Author, XSLT 2.0 and XPath 2.0 Programmer's Reference