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Goeff is right - you need to increase your exposure range and your tonal range. Software is not your problem.
There are a fwe golden rules for HDR. First off, never change the aperture. It affects sharpness and depth of field and that will make your HDR images look soft and they'll lack detail.
Secondly, never alter the ISO as you'll introduce noise and minor A/D conversion artefacts which will affect microcontrast and weaken colour.
Auto bracketing is rarely (if ever) suitable for HDR. Most people's HDRs look flat because you're only ever getting 3 exposures and they're usually not far enough apart. If you want to get HDR photos to look good you need to use either aperture priority and exposure compensate or manual mode and just adjust the shutter speed.
Put it this way: +2, 0 and -2 is never very good. +2, +1, 0, -1 and -2 is far better. You'll get more tonal range, better contrast, more detail and better colour.
On top of that, you need to actually work out if your -2 is dark enough or your +2 is bright enough. For the best results the darkest (most underexposed) shot needs to be about 2 stops under the highlight clipping and the brightest (most overexposed) shot needs to be 1 stop over any shadow clipping. For an average landscape scene (and I've shot a lot of HDR) that is usually something like a +4 down to a -6 or-7 with each individual stop in between (+5, +4, +3, +2, +1, 0, -1, -2, -3, -4, -5, -6, -7)
Any software can only work with the image files, and their associated luminance values, that you give it. If you don't give your software enough data you won't get good results.
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