There are many good pickup systems out there (though less for ukuleles) and every year or so brings new innovations in the relatively young space of acoustic amplification. We've seen most of them, and after what some would call an unreasonable amount of experimentation, we settled on the MiSi Simple Jack preamp with Fishman Matrix pickup. This is a more pricey piezo pickup than MiSi's standard LR Baggs element, but we find it quite pleasing to the ear and easier to achieve volume balance string to string.
At 1 oz. with pickup, bottom line there is no lighter active system on the market which means that you won't hear the difference between an acoustic or an acoustic/electric Blackbird unplugged. That is huge for smaller instruments! MiSi achieved this ultralight feat via a rechargeable super capacitor versus a battery and allowing for a shockingly small and light electronics package (one minute charge=16 hours of playing time). Some other systems use a watch battery which is loads better than the paper-weight of a 9v that has been the industry standard for years. That said, those watch batteries are often mounted to the soundboard which can affect tone.
Finally, it nice to have both volume and tone control. MiSi offers volume/tone while other low profile systems offer volume controls at best. The tone control doesn't do that much honestly but it can help 'round over' the sound via the instrument.
Ultimately acoustic pickup systems should be chosen based on the needs of the player and while our standard set-up is versatile and will serve most well, Blackbird is able to install all sorts of difference systems based on use-mode.