Having been in Belgium and The Netherlands two weeks ago I do confer with what the OP has written.
Station dwells in particular take quite a while - When I took an Intercity train from Charleroi-Central to Brussels-Midi there was a 6 minute dwell at Braine-L'Alleud, which added to the sluggish feeling of the line, with most of it having a 120 kph limit with one or two short sections of 140 kph.
Lots of dwell time (padding) has been added to the schedule of line 124 because of the works that are currently taking place, which are sometimes causing unexpected delays. By the way, 7 km of quadrupled track come in service end of next month. The line is a bit curvy, so high speeds are not possible everywhere , but a mix of 140 and 160 km/h should be in place after the works.
One nagging thing about SNCB and Belgian railways in particular is how inconsistent the offering and experience is. On the one hand there are absolutely incredible stations such as Anterwerpen-Centraal and Liège-Guillemins, fairly solid stations such as Brugge and Leuven, but also a lot of very unpleasant and run down stations such as Brussels-Midi and the un-refursbished parts of Mechelen and Ghent-Sint-Pieters.
SNCB has been deeply criticized for building "extravagant" new stations so now resources go for stations that are lacking in functionality or capacity. Mechelen and Gent are in this case. Those un-refurbished parts you mentioned should have disappeared in a few years. Brussels Midi is a special case. Rebuilding this station would require to take out of service one platform and two tracks at a time. With 1200 trains per day, this is not possible with the current track layout. Those modifications are slowly taking shape. Probably 10 more years of preparation work will still be needed before station refurbishment can begin.
The quality of rolling stock is very inconsistent as well, ranging from very nice locomotive hauled trains running on the fast Oostende/Kortrijk to Liège-Guillemins/Welkenraedt/Eupen services, to the commuter-specified Siemens Desiro trains being used on the Liège to Luxembourg services. Having said this the introduction of M7 trailer and motorised carriages is making the allocations of trains on secondary Intercity routes much more consistent.
Had Alstom do its work properly and delivered a reliable M7 vehicle, SNCB would have ordered the 1400 cars that were initially foreseen, and most of this inconsistency would be on its way out. Unfortunately this is not the case and SNCB stopped the damage at half order. We will now have to wait for the completion of the next order to see all already too old equipment disappear.
Regarding Liège Luxembourg, I agree with you that it is very unfortunate, but there really was no choice. Local people asked for an hourly service, and SNCB agreed only if operational costs could be reduced. Desiro was the only available solution.
There are also quite a few lines where the linespeed could be raised. In particular the long 140 kph sections on the main line between Brugge and Brussels make the journey seem a bit tedious. I understand that line is in a state of flux, with ongoing four-tracking and the replacement of the legacy portal-based electrification with single track cantilevers, so maybe an increase in linespeed to 160 kph or maybe even 200 kph as seen between Brussels and Leuven would make the journey quite a bit quicker.
Bruxelles Gent should be 200 km/h, one day. It will require an almost total rebuild, as tracks are too close and it needs a new catenary. Gent Brugge will be 160 km/h only : 200 was planned but after lots of work was already done, regulations changed and most of the work would have to be remade almost from scratch, notably many intermediate stations. So 160 it will be...
But in any case, speed increases are not the top priority for Infrabel right now. They managed to reduce the number of signal towers from 200 to 10 in 20 years, install bidirectional automatic block everywhere, eliminate all mechanical and electro-mechanical (relay rooms) signalling, and will have the whole network covered by ETCS at the end of this year. Plus the quadrupling of most lines radiating out of Brussels. It's a small country. Higher speed delivers minimal time gains over short distances. So it's seen as a luxury best kept for until after many more urgent problems are solved.
My final point of complaint, as with most continental European countries is that cross-border connectivity leaves a lot to be desired. There are countless examples of cross-border sections of track between places either side of the border that are either closed, mothballed, have no passenger service or where a useful Intercity service terminates at the very last or last major station before the border. Belgium has made a great effort in building cross-border high speed railways, however, the services that use them leave a lot to be desired, with trains selling out weeks in advance (eh hem, Eurostar Red), being eye-wateringly expensive (eh hem, all Eurostar services) or not being frequent enough (Brussels to Cologne and Lille really ought to have two trains per hour). The introduction of the NS Eurocity Direct from Brussels to Lelystad is a great step in the right direction though.
Brussels to Cologne is being worked on. Watch the delivery of the new HLE17...
Eurostar, blame SNCF, not us Belgians...
Otherwise, at regional level, we have two hourly connections to Lille, one bi-hourly to Maubeuge, 3 hourly to Luxembourg, one too Aachen, one to Maastricht, and one to Rosendaal. I think it's way better than most neighboring countries manage. I'll also mention that all those cross border relations are operated by SNCB rolling stock. None of the neighbor networks are able to provide anything.
Ah, and by the way, the slow train to Paris is an overwhelming success. SNCB would love to introduce more frequencies. SNCF said no.