For our new product re-engineering, we are in the process of selecting the best framework from Java. As the consideration is to go for database agnostic approach for model, we are working on options between Struts + Spring with iBATIS or Hibernate. Please advice which is best as both offer persistence.
iBATIS and Hibernate are quite different beasts.
The way I tend to look at it is this: Hibernate works better if your view is more object-centric. If however you view is more database-centric then iBATIS is a much stronger choice.
If you're in complete control of your schema and you don't have an extremely high throughput requirement then Hibernate can work quite well. The object model makes for fairly convenient code but at a huge complexity cost.
If you're dealing with a "legacy" database schema where you need to write fairly complicated SQL queries then chances are iBATIS will work better.
HQL (Hibernate Query Language) is another language you'll have to learn and even then you'll probably find cases where you still need to write SQL. What's more, chances are you will at some spend half a day figuring out the right combination of XML, properties, annotations, etc to get Hibernate to generate a performant SQL query.
There is no universal "A is better than B" answer for this question.