Getting back to the original post, this is a problem not just with the ipad but will all tablets. They all - apple, Android, etc, seem to have problems translating some traditional PC platforms. I was hoping the BB Playbook was going to change things with its flash support but having tried it it seems rather clunky as well.
Apple are not likely to come up with solutions to most of these issues as they want to drive all of their users through their Appstore channel. I have quite a few Apple products - Ipods and computers - but I must admit the company's efforts to lock everyone in to the Apple environment does grate a bit at times.