I'd certainly like to see another game in the series - but I have a feeling they would want to change the format. Raven wanted to do something new with JA, and it worked to a certain degree (the tiered mission format - okay in principle but slightly flawed in the execution). Many people have already complained that JA was too similar to JO in terms of the gameplay dynamic, and some simply viewed it as an expansion pack - which is a bit unfair IMHO. Nevertheless, the whole game industry at the moment seems to be trying to reinvent the wheel for no good purpose (other than to widen the target markets), so I would imagine any more games in this series would undergo some fundamental changes. An engine change is pretty certain for starters.
There's nothing to say Raven would even be involved in another instalment. Lucasarts can engage any other developer they like - or once they've cut their teeth on Republic Commando, take the whole thing back in-house to develop on the Unreal tech.
I strongly doubt that they would build a completely new engine from scratch. Coding a new engine is no simple task, and can take years of development. Just look at the Source engine from Valve - they've basically been working on it since Half-Life was released. Building an engine takes time and resources - and you have to be pretty certain there is a big payoff at the end to justify the costs. It's far more economical to take an existing engine and modify it to suit your needs.
Who's to say? Only Lucasarts has the answer...