I have not seen prep TLC used for some years now. Prep HPLC is almost all Mass directed today, which provides a massive step up in resolution and purity achieved. It is not unusal to get a 90% + pure samples post prep HPLC-MS. Prep TLC requires a lot of manual work, watching the sample, and gives you nowhere near as good purity and resolution. TLC is much cheaper to buy and operate, and doesn't need a whole lot of training. That may be your key differntiator.
Who says both methods cannot be used sequentially. For instance, column chromatography precedes TLC in the separation of phospholipids. The techniques are slow and require good skill with column preparation, flow rates, and solvent removal. The phospholipids are subsequently quantified by TLC and wet phosphorus analysis. The best method is determined by sample type. Preparative-layer chromatography (PLC) is an effective and easy means of obtaining small quantities of compounds from natural mixtures, which can then be used for different purposes – for example determination, by spectroscopic methods, of the structure of the compounds isolated or investigation of their biological activity. PLC can be used not only for isolation but also for on-line purification of plant extracts rich in non-polar (lipids, chlorophylls, waxes) or polar (tannins, sugars) ballast, as a method of sample preparation when purification in one step is not sufficient for isolation of a fraction before GC or HPLC. Preparative-layer chromatography can be used as a pilot technique for preparative column chromatography, in which both optimization of system. Colum,n chromatography could also precede TLC. So, everything boils down to nature of sample. Please visit the links below. https://www.nacalai.co.jp/global/cosmosil/pdf/Technical_Notes4.pdf http://www.actabp.pl/pdf/3_2016/2016_1369.pdf. http://www.us.edu.pl/uniwersytet/jednostki/wydzialy/chemia/acta/ac18/zrodla/18_AC18.pdf. https://www.banglajol.info/index.php/BJP/article/download/28185/19914
In column chromatography, the separated band may contain a single component or a mixture of few components of similar polarity in a given mixture. This can be ascertained using TLC. If a mixture, preparative TLC is the better technique to purify further to get the desired component. HPLC is also a good technique, especially preparative HPLC, where the purity of eluted component is controlled using Mass spectrometric detector.