I have no problem with Timeships or cloaking devices overpowering any challenges, for two reasons:
1. No one has said exactly how
reliable these technologies are. Based on what we've seen of Romulan and Klingon cloaks, the tech is very useful but definitely doesn't seem to be a trump card, by any means - shields are down if the cloak is up, can't fire phasers and wouldn't want to if you could, since that could be tracked back to reveal your location. (Photorps
could be preprogrammed and pushed out the back of the ship, powered down, while the ship moved away, and then power up to go to their target - but that would also mean there would be a moment when they would be powered and at very low velocity, since they wouldn't be
launched. Easy pickings for an opponents phasers. I suspect that's why we haven't seen that done.) Timeships might have all sorts of problems we don't know about - like if you miscalculate your course, you end up moving unpredictably between parallel universes instead of back or forward in your own, or risk moving through space instead of just time and coming out in the middle of a celestial body or plain
lost.
2. An interesting potential series plot that combines using the two in a way that generates challenges has occurred to me - and is one of the missions my fanfic Enterprise very occasionally undertakes: historical disaster retrieval missions. Things like mocking up corpses that would pass examination by the medical community of the time, and travelling back to rescue the people who "died" on the Titanic, replacing them with the mock-ups. Sounds easy enough if everything goes smoothly, right?
My main problem with timeships is the containment issue: If Starfleet starts building timeships in the 26th century, then maybe they'd keep the number very small - say the aforementioned 13. But, by the 28th century, the tech would be all over the place - everybody would have it. You could time travel in your civilian freighter. Now, if everyone can time travel in the 28th century, they can go back to 16th century Earth (to pick a time at random) to see what it was really like - and ultimately they will. A lot of them. And they will continue to do so, until 16th century Earth is just overrun with future tourists and starships parked all over the place and in orbit above. Tourists paying for things with quatloos and gold-pressed latinum and all sorts of alien currencies, wagging their tongues about things that the locals don't know about yet, and getting their ships stolen. Before long, you've got people from the 16th century visiting the 64th century and the 10th century and creating the same problems all over and over again. Not to mention that now the Europeans who were supposed to settle North America have been forced to return home by Native Americans armed with quantum torpedoes, given to them by Chakotay's decendents.
It all becomes a big mess, really. Unless there's some mechanism to keep it from happening. And the mechanism would have to be perpetual, or the problem would just start when it stops.