My roleplaying game takes place in the 25th Century so we have explored some of these possibilities.
1.) Positronic Chips - Based upon the technology used in Lieutenant Commander Data and the research of Commander Bruce Maddox, Starfleet Engineers have been able to upgrade Starfleet vessels with positronic circuitry increasing their calculation capabilities and data storage.
2.) Hybrid Warp Core - exactly as suggested above.
3.) Tachyon Torpedoes - Tachyon Torpedoes are designed to disable the power systems of an enemy starship rather than destroy.
4.) Phoenix Torpedoes - Phoenix Torpedoes can bypass alien shields; however, they are volatile.
5.) Masking Circuits - Masking Circuits are the Federation outgrowth of the Treaty of Algeron. Rather than develop cloaking technology the Masking Circuitry can be used to minimize a Starship's sensor profile.