Nitin,
This question gets asked from time to time and the key portion of understanding the differences is that MyEclipse is actually built ontop of WTP. So any feature WTP ships, we ship. So the trick is to figure out if there are any killer features in MyEclipse that you must have, like the visual web page designer, Matisse4MyEclipse, Hibernate & Spring integration and reverse engineering, database explorer, UML designer, JavaScript development and debugging or any of that. More features are listed here: http://www.myeclipseide.com/ContentExpress-display-ceid-15.html