You have a couple of possabilities:
1 - use an "Amber" like multi-verse rule so that as well as travellin gin the time-stream, they are also travleiing between different universes with differing physical laws. In some places, guns won't work, and electronics might be dead or simply unreliable. Its places like these that the fighter will shine.
2) Include plenty of enemies that can only be hurt by certain things. If (eg) you have zombies that needs to be hacked apart with slashing damage rather than shot at, with the bullets passing harmlessly through their rotten flesh, the sword will rule over he gun.
You can do the same with technology - a bad0guy might have some form of shield that stops high velocity items like bullets, but can still be penetrated by a sword (cf Dune), or even an EMP device that temporary disables electronic devices.
3) You could even rule that the changes to the time stream being caused by the bad-guys affect the technology from further up the time line. The heroes might need to repair that damage to get access to their own high tech devices, simply because the damage to the time-stream had previously prevented it from being invented.
4) Batteries and bullets. Where are you going to re-charge your cybernetic arm in 1066? Who will sell you explosive bullets in 1492? Make sure your characters know these things might be in limited supply.
Or, all of the above, of course. The trick will be to use these tactics just enough to give all of your players an equla chance to shine.