A legitimate point, about all that technology!
But you can always find some limitation. Your starship doesn't visit a planet hundreds of lightyears from home, but at the edge of the galaxy itself. You're confronted with rivals with an equal technology to your own. New diseases rise to take the place of old ones. Turns out slipstream is even less stable than anyone thought. Yeah, you can transport between planets but the conditions have to be perfect. The phasing cloak turns out to offer no real defense against anyone who figures out the polarity of the phasing field and simply adjusts their weapons accordingly. If all else fails, have Starfleet start putting some real teeth behind enforcement of the Prime Directive--anyone caught violating it gets a one-way ticket to a mind-wiping facility, then rehabilitation in some frontier colony. That creates some real tension.