The FID is a great detector and can give LODs for many compounds below that which you can obtain with an MSD. However, the FID is blind to some compounds as well. So, if you are looking at chromatograms for specific target compounds that contain carbon (and are not one of the compounds that is nondetectable by FID), then FID may be the perfect option. If you are looking at unknowns or potential unknowns (ID confirmation required) then a MSD can be very helpful. The MSD is the nice toy in the toy box - but it has a cost for purchase, requires more time consuming maintenance that the FID and (unlike the machines on CSI) does not necessarily lead to definitive identifications of unknown compounds.
If you have a requirement for an instrument that will have an MSD, consider whether you need the FID at all. An MSD is best left up and running. Thus you will want to leave a column installed and carrier flow – in which case you have a column that is ready to perform analyses. Years ago I worked in a lab that had a number of GC-MSD systems and each was purchased with second split/splitless inlet and a FID installed in the instrument “Just in case.” I recall instruments being retired with neither the second inlet nor the FID ever having been used.
Where I mentioned that you can get lower LOD's on many compounds with the FID, take note: This becomes a bit of a problem because at very low levels, you have a greater risk of confusion with low level interfering compounds - and selectivity and/or compound confirmation becomes very important - driving you to an MSD where you have detection problems with it. The solution is changing sample preparation rather than to using the less expensive detector - and because you are concentrating background garbage as well as analytes, the MSD may still be required for selectivity and compund confirmation.
In that lab we did have instruments with the gas stream from a single inlet split to two (or more) detectors. While this approach allows for flexibility in use – the sample is split (decreasing sensitivity) and the additional plumbing becomes an additional source of maintenance issues in the instrument. You can install columns into each of two inlets, with one column running to the FID and the other to the MSD. Either both columns are of the same type or you run into the issue that the temperature limits for both of the columns must be observed to prevent damaging the more fragile column.
If you purchase the instrument with both MSD and FID, plumb in the MSD only until you determine that you have a need for the FID as well. It keeps life simple – and you have the FID, just in case.