It depends on the tasks. If it's a task that makes full use of 4 cores, the i5 may do a little better but again you have a 500-600mhz speed difference in favor of the chip that has a 5-10% ipc improvement and is at least 2yrs newer. It's not really a fair comparison for that reason. A faster i3 with mainly 2 cores loaded will be faster than an i5 with four slower cores because the extra 2 cores aren't being used. A faster i3 with 2c/4t vs a slower i5 with 4c/4t may come close to the i5's performance where all 4 cores are fully loaded.
Real cores beat out ht, so 4 real cores vs 2 cores with ht is more powerful - at the same speed. Start gimping one or speeding up the other and it alters the equation. A 4c/8t i7 like the 6700k can outperform a 4c/4t i5 if it's fully utilized. Then again a 5960x with 8 true cores can outperform a 6700k, even with ht turned off - 8 true cores vs 4c/8t hyper threading. Provided it's fully used and provided the speeds are similar. Turn the 5960x down to 2ghz and bump the 6700k to 4.8ghz and sure the 'weaker' cpu may actually be faster.
Between the 4460 and 6300 I'd rather have the i3 also - for those games. For other tasks I might want the 4460. There's a roughly $30-40 difference. There's also roughly a $30-40 difference between the 4460 and 4690k so overall I'd rather have the 4690k and oc it. The i3 6300 won't outperform it, either multithreaded or single threaded.
Everything has to be considered, there are no simple rules. Clock speed isn't always the deciding factor, core count isn't always the deciding factor, generation isn't always the deciding factor. Programs change from one to the next even from game to game. There's no simple 'ht good' or 'ht bad' or 'gaming'.
People need to consider what games or programs they plan to run then consider which cpu will run them the best within a given budget. There's no need for an i7 or fx 8350 for a game that uses mainly 1-2 cores. If the game scaled to 4 cores or beyond then an fx 8350, i5 or i7 should be a consideration provided the gpu isn't the weakest link.
A similar effect happens in video encoding, many people consider the xeon 1231v3 to be the obvious better choice. Most video encoding programs can make use of multiple threads so hyper threading offers an advantage. Clock speed also plays a role though and a 4c/4t from the same generation of cpu's (no ipc advantage) can encode just as fast as a 4c/8t xeon when the i5 is overclocked a good deal. If it were strictly stock to stock, yes the xeon would be better thanks to ht but ht isn't the whole picture. One has ht, the other has clock speed and in the end they tend to balance out. Much like we see with the i3 vs i5 here.