I think so.
Star Trek Online is an online game, and could offer a very competitive environment. However, the overall game structure isn't flexible the way a role-playing game and GM are. This is true for both PVE and PVP. The game's AI can only react so much to players before it falls apart or has to be made more ruthless, more advantaged, in order to provide a challenge. But, on top of that, the typical equipment treadmill for PVE means there will be disparity between players and their ability to obtain said equipment (be it time and/or money). All things being equal, the better gear will win.
Moreover, what makes an ability loads of fun and useful for PVE might be incredibly broken for PVP. This was an issue for City Of Heroes, where players were incredibly powerful for the PVE game, and it translated poorly to PVP. Guild Wars: Eye of the North added a PVE only skill or two, acknowledging that trying to balance for PVP and PVE wasn't as interesting as having some stuff being gloriously, wonderfully broken for PVE. And again, there's no GM or Referee here to intervene. PVP as War might not be a viable option. So, what about PVP as Sport?
Let the games begin.Red 5 is altering their PVP structure in a way that I think Cryptic might want to look examine. Likely they've discussed it, but I'll say it anyways. Formalize it. Because PVP as War cannot be fully expressed within the game, and makes balancing difficult, embrace PVP as Sport in addition to the current formats.
Sport PVP would require that all characters operate with equivalent equipment, weapons, and devices. All items would need to be commonly available rather than being drop dependent, earned as rewards, etc. By equalizing everyone in this regard, it lets players focus on their playstyle, teamwork, etc. By keeping this equipment separate from the normal PVE equipment, it can (and should be) evaluated more often for balance issues, tweaks, etc.
Level/Rank disparities can be addressed via auto-leveling or, where appropriate, point-limits. Players/Ships at rank X are worth Y points, with a team having Z points, for instance, similar to a wargame such as Warmachine, Warhammer, etc. A lone Vice Admiral player going against a dozen or more Ensign-level players (space or ground) might be an ugly fight, but could be workable. Again, this would need examining regularly. Even if HP were normalized, there would still be a significant difference in available skills/stats.
PVP Tournament formats would need establishing; certainly, players being able to run tournaments easily would be beneficial to the PVP community, I believe. Setting team size/point limits, brackets, seeding, and more would be very helpful. Official tournaments could involve simple entry fees going towards a larger pot (nothing ventured, nothing gained). Such fees could be in Energy Credits or even Dilithium (allowing for a degree of monetization). Rewards ought not be PVP-based, but rather PVE or cosmetic. Ideally, it ought be an activity that can earn Experience to provide a valid means of progression.
All of the above would need to be in addition to the current PVP structure, not in place of. Arguably, PVP could be set into seasons, with adjustments made between seasons. Having the PVP equipment being purchasable via Zen or Dilithium could help offset development costs, and provide a barrier to players prone to harassing others (in theory). Seasons could well have rewards of their own for active participation.
Just my thoughts.