There'll be CSM's, I dunno about Skipper missiles, since cloaking isn't completed yet, but they could be implemented via scripting.
About the phase shields: In the WC universe, there's a constant race between shields and weapon technology; in WC2, shield tech was more advanced than weapon tech, and a few years later in WC3, weapons were developed enough to damage shields. Two decades later in WCP shield tech was more advanced than wepons again, and so on.
In WC3, only the Victory and the Caernavon class frigates were really old, while ships like Talahasse class were rather new.