i think they should take no chances and do the borg for ST3 in 2016 (Star Treks Skyfall)
-Although the borg have been done to death on TNG (& VOY/ENT) and in a prior film, they are firmly a TNG era villain and we have never seen Kirk and Co have anything to do with them (bar a comic in the Star Trek Manga series and Shatners 'The Return'). Fans would obviously be intrigued with how Kirk, Spock would deal with the borg threat (almost a TOS vs TNG/Kirk v Picard thing going down)
-post Q Who/BOBW part 1 (when the borg were at their most menacing) they always seemed to have a spokesperson which lessened their impact somewhat so while initially it would seem they are treading old ground it would actually be fresh if it was a more alien non Locutus/Lore/Queen led borg vs Kirk and Spock. (so it would really be a remake of Q Who but with TOS characters sans Q)
-the budget would be in the $150-200m range (First Contact = $45m in 1996) so we could see a totally new version of the borg with todays FX. a far more frightening interpretation more Ridley Scott/HR Giger style pushing the boundaries of the PG13 rating and leaning more toward horror Sci Fi - Star Trek does Aliens/Terminator (like FC but even more so)
-We havent seen the origin of the borg yet or the borg homeworld so maybe the origins could be explored abit but still keep it vague/lots of mystery alien-ness (like Ridley Scott did with Prometheus). could Vger even be involved? (ok it wasnt too popular but TMP was the biggest box office Trek movie before STID & Vger appears in the Nero comics and im sure there was a novel that ties Vger into the origin of the borg - Shatners The Return? )
-There was a hint of the borg in ST09 - Neros ship, ok that was just a reference in Countdown but the design of the interior and green hues of the stations certainly had me thinking borg technology (could the borg of the 23rd century have detected the narada while it was about and be on their way to take over the federation? Or Could its remains have appeared in the delta quadrant? Which could also account for any appearance differences - borg of 23rd century could look different to TNG era borg) plus B Orci & AK refer to Best of Both Worlds on the final page of CD
-Robotics/cybernetic type aliens are in vogue thanks to the continuing installments of Transformers. U can see its influence on many recent SF films post 2007 - Terminator 4 (transformer like terminators designed to appeal to the PG13 crowd), Trek09 (neros ship), Cowboys/Aliens, Battleship, Skyline, Avengers, Pacific Rim, MOS etc
-The borg also have a strong zombie vibe - zombies are bigger than ever now due to Walking Dead and WWZ
-The studio will want to capitalise on the popularity of Trek to ensure MAXIMUM box office - going with a new interpretation of a previously established villain like Khan in STID will certainly help to do that (although they should publicise the villain the next time instead of hiding it). Paramount had big box office success with First Contact, far more so than any of the other TNG films (or Trek V and VI for that matter)...the main reason behind its success was The Borg...and Best Of Both Worlds part 1 is regarded as TNGs finest hour (next to Yesterdays Enterprise) and just about changed American dramatic television (the season cliffhanger)
-both Trek09/STID have a kind of 'greatest hits' of Trek thing going on (abit like the Brosnan Bond films) and are focusing on the more popular villians in Trekdom as opposed to anything lesser know or totally new. the Borg are one of the most popular Trek villians (along with Khan, Klingons and Romulans)..and certainly the most popular villains of the TNG era Trek (i dont believe we'll see any of the lesser know Trek villians like Cardassians, Breen or even Andorians or Gorns take centre stage in any sequels - beyond a cameo or supporting part)
-The Klingons, while a natural villain for the 3rd movie after their cameo/foreshadowing in STID (and esp one for the 50th ann - like they were for the 25th ann Trek VI), have over the years become seen as more of an ally to the federation/Starfleet due to TNG (plus the 4 TNG films with worf, not to mention Trek VI which we saw the federation and the klingon empire battle it out for peace) so it may be difficult having them go back to full on sole villains. (which might have to be another political style film like VI). Might be best if they remain an uneasy threat in the background or even have the film start with a Federation/Klingon war - but then the klingons have to team up with the federation to fight the borg (thus fast tracking their alliance a good 30 years early and foreshadowing the eventual peace in TNG). Anyway didnt Kirk and Co prevent a federation/klingon war in STID? (which was similar to VI). plus i dont think they would be as interesting and as scary a threat as the borg - esp when you take into account there may not be a forth film with the nu Cast (the cast becoming more difficult to secure, the idea of a trilogy wrapping up the movie series for a few years while trek goes back to tv, in which case a 4th film way down the line would probably feature a new cast/new era) so if you asked any fan or even a person with a vague knowledge of Trek - 'who would you rather have as villains for the next (and possibly final) film - the klingons or the borg?' i think most would say 'borg.' Also the klingons have featured alot in the previous films (main villains in III and VI but also feature heavily in V and VII)
-i imagine something special will be done for the 50th anniversary in regard to Treks history (like Skyfall/Dr Who 50ths) so perhaps something involing the borg messing about with time travel/alternate realities could be a possibilty? (the borg know about/have dealt with timetravel/alternate realities) maybe even something involving the nu Crew with Picard and the TNG (&7of9) 'Days of Futures Past/Yesterdays Enterprise' style? (the YE two crews thing hasnt been done on the big screen yet - and the team up thing is all the rage now - Avengers/Batman vs Superman) - It will have been 14 years since Nemesis, enough time to heal the wounds and have fans anticipating some TNG again! (2016 will also be the 20th anniversary of FC). So a kind of all encompassing Trek film for the anniversary...maybe working in Nimoy again, and Shatner finally, and maybe even somehow concluding the JJverse as a self contained trilogy (like TDK trilogy)