I tested a couple of versions of jupgrade, but I never had it to migrate more than parts of the J 1.5 site.
I absolutely recommend SP Upgrade. I migrated more than 40 Joomla sites, so this component made the work much easier.
I suppose you mean duplicate alias and not ids. Ids remain the same.
There is a new rule now in Joomla! that was not in version 1.5. In order to be compliant with SEO and Google requirement to have one content per one url, and given that alias are used to build the urls, you cannot have the same alias under the same parent. That goes for menus, articles etc.
Therefore SP Upgrade when identify such case, automatically add a random qualifier to the alias. Even if you try to manually edit it from back end, you will see that Joomla! will not allow it.
It is probable those duplicates comes from your trash. Therefore before migration it is suggested to delete and empty trash for any not needed items.