Fenix has a design philosophy of building their lights simple in order to give you the brightest light and the longest runtime, with greatest reliability. There is no light in their lineup that has any programmability, let alone memory retention; there is no light of theirs that will ramp. The interface on each every light is very straight forward and simple. Even the body design says simplicity. Except for their tactical models, the lights have very little knurling or just enough.
Most of the Fenix models do not give you the options of using a variety of different rechargable formats, especially lithium rechargables; again simplicity in design. When lithium rechargables will operate in a Fenix model, often not all light levels are avaiable. However, there are a few models that allow the use of different battery tubes and either CR123 or AA usage.
The NiteCore philosophy is different. Although they try to create this tactical image, I would say they are more a user adapted light. Instead of the user having to adapt to the fixed light levels, and fixed cell options, Nitecore tries a bit more to let the user adapt the light to his needs. Rather than being stuck with only certain light levels, NiteCore offers a user a broader choice of light levels, including lower lows that can be selected and saved in a user definable mode if he wishes. Ramping light levels is an option on all of the models. All of their lights offer you a chance to use lithium rechargables and have built in protection circuits to even let you use unprotected cells. Most of the NiteCore models are not as bright as the brightest of the Fenix's, but they do offer lower lows which many people want. The NiteCore look is a bit more aggressive; knurling not at all lacking. Runtimes, while acceptable, are not comparable to the best runtimes in the Fenix lines. With a bit more complexity in the design of some of the NiteCore models comes the cost of reliability should you not maintain the lights properly, or operate them properly. The split ring on the PD series is especially prone to problems if the contacts are kept scrupulously clean. If you don't apply steady enough pressure to the PD switch, it may misfire changing modes, or shutting off entirely. It takes a bit of practice to use these lights properly, unlike the more straight forward Fenix models.
So to say which company is better is difficult to answer. It all depends on how your needs match up with the design philosophy of each of these companies. If you need a simple straight forward, no nonsense, design with bright, long runtimes, Fenix will probably have a light for for you. If no light with a fixed light levels perfectly suits you and you wish to use rechargable lithiums rather than primaries, then you will probably need to look at a company like NiteCore to provide you with a light that you can customize to your own needs.