I took a look at the default template for an Atom feed, introduced in Movable Type v2.65. This template seems to be where much of the new stuff fits into the new release.
Within the template, we see that there is a new date tag, MTEntryModifiedDate, to make use of the modified field on entries. Taken at face value, the introduction of this tag would seem to invalidate the use of the LastModified plugin by Staggernation. Realistically, you might want to continue using this plugin, as it also offers a conditional tag that you can use in your display to include information only if an entry has been modified.
Another nice addition to this release is the introduction of the utc attribute on the date tags, specifically as it is used on the MTEntryModifiedDate tag. It would appear that this can be used on all date tags, which may mean you can get by without another Staggernation plugin, UTCDate. Once again, make sure this is what you want to do, as the plugin does offer some additional functionality that is not present when you use the attribute – notably the inclusion of an offset for that tag or an indicator that determines if you’d like to use daylight saving time or not.
There is also another tag introduced, MTIfNonEmpty, that you pass a field name. If the field is not empty, then the enclosed information is included in your template. In the Atom template, this is being used to include category information if there is a category assigned to the entry. This appears to be functionally equivalent to the MTIfNotEmpty tag you can get with the IfEmpty plugin from Brad Choate. Just be careful – the MTIfNonEmpty version appears to require the leading “MT” on a tag (ie, MTEntryAuthorURL), while Brad’s plugin does not (ie, EntryAuthorURL).