I'm no design engineer but space in one big reason. F-16s landing gear is in it's belly so it stands taller when measuring ground clearance from the wing.
JF17 doesn't have much space in the belly so landing gear is attached to the wing just like Mirage. However Mirage is a low wing aircraft and flat underneath so it has more clearance available to carry larger or oddly shaped weapons.
I'm sure the designers had their reasons for placing everything where it is and keep in mind the aircraft was develop on a $500 million budget, that's tiny compared to what other countries spend developing their aircraft.
A key consideration for having shorter ground clearance is also ease of accessibility and servicing the aircraft. That translates to most panels that in easy reach for technicians and ground crew and thus potentially quicker turn around time.
Space on a smaller airframe also makes having shorter landing gear beneficial as any savings can translate into more room for fuel.
Check out how low the wings of the Saab's Gripen are in comparison, another small jet that is famous for ease of maintenance and quick turn around time in the field.
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Of course Gripen is a better designed aircraft in comparison to the Thunder due to the greater experience Saab has in aerospace design. But to offset the lower ground clearance just means you need to develop more compact smart weapons, which is now the trend anyways in any modern air force.
With the JF-17's ground clearance, I think the issue is more that we lack appropriately sized munitions than anything to do with the JF-17 itself. The Ra'ad v1, for example, was designed for the Mirage III/5, and we did not take the JF-17 into account as, at that time, the JF-17 was not a near-term factor. Ditto for H2/H4.
However, with the Ra'ad 2, it seems like Pakistan is investing more in developing its SOW stack. There is a chance that the JF-17 may be able to carry it. The PAF can continue investing along these lines, e.g., look at a 'Ra'ad Lite' (similar to Turkey's SOM), new-gen glide bombs to replace H2/H4, and other ideas too (e.g., a SPEAR-like ALCM can help too if we can economize it).
@JamD @SQ8 @kursed
That said, for the PAF, the JF-17 is an MVP (Minimally Viable Product) in design and role. You'll notice that its precision-attack, anti-ship, long-range air-to-air, and so on are
just enough to fight in our region. Now, as the region got more sophisticated, the PAF added more features to the JF-17 so as to maintain the MVP status (e.g., AESA radar, HMD/S, ECM, etc).
This situation is likely due to a lack of funds more than anything. If the PAF could "go ham" on the JF-17 by loading it up with bells and whistles, it would. In fact, when the fiscal situation was relatively better in the 2000s, the PAF spoke to Thales and MBDA for the RDY3, MICA and TopOwl.